Let's ignore, for the moment, the point that fiction is an exploration of human interior spaces, and that sometimes a spaceship or a princess is a metaphor; science fiction and fantasy are genres famous for their departure from the plane of mundanity, and usually a spaceship is just a form of transport between inhabited worlds ...
Let me tell you what makes me yell when I kick the tires on an SF/F novel these days.
There is a term of art that developed early on in the field of SF criticism: willing suspension of disbelief. When we read a work of fiction we are taking, as a given, statements that build upon one another to construct a cunningly plausible lie. We suspend our natural disbelief in things we know to be untrue, for dramatic effect cannot withstand the scorn reserved for falsehood. However, there is a limit (different for everyone) to the number of lies we can stack Jenga-style atop one another before our disbelief can no longer be held in abeyance: on reaching this point, the willing suspension of disbelief fails and the tower of implausibility totters and collapses in our minds.
Disbelief can be shattered easily by authorial mistakes—one of the commonest is to have a protagonist positioned as a sympathetic viewpoint character for the reader behave in a manner that is not only unsympathetic but inconsistent with the protagonist's parameters. But there are plenty of other ways to do it.
Certain patterns are guaranteed to make me throw a book at the wall these days (or they would, if I wasn't doing almost all my reading these days on an iPad), or at least stop reading on the spot. One such pattern is sometimes described as "the seven deadly words"; when you can say of a story "I am not interested in these people," the author has failed to hook you on the human content of their drama, and unless they're compellingly brilliant on another, inhuman, level—for example, the works of Olaf Stapledon or (some of) the works of Greg Egan—then that's it, game over. Another pattern is "this is pointless and tedious" (although it's even harder to define than "lack's human engagement"), and a third might be "this makes no sense" (on any level, including deliberate surrealism).
But then we get to more specific matters: specific shibboleths of the science fictional or fantastic literary toolbox that give my book-holding hand that impossible-to-ignore twitch reflex.
(Caveat: I am talking about books here. I basically don't do TV or film because my attention span is shot, my eyeballs can't scan fast enough to keep up with jerkycam or pull in enough light to resolve twilight scenes, and my hand/eye coordination is too crap for computer games.)
Asteroidal gravel banging against the hull of a spaceship. Alternatively: spaceships shelting from detection behind an asteroid, or dodging asteroids, or pretty much anything else involving asteroids that don't look like this:
That pock-marked potato, asteroid 243 Ida, is just under sixty kilometers long. (You could fit London onto about half of its surface area, with room left over.) Asteroids are not close together—bodies wider than 1km are, on average, about 900,000km apart—more than twice the distance from the Earth to the Moon. Smaller bodies tend to be gravitationally captured by larger ones over time (we're talking billions of years here); did you wonder where that rash of craters on 243 Ida came from? If you think of that scene from "The Empire Strikes Back" when you think of asteroid belts you are thinking of a whole bundle of nope.
Comets ... they're a bit more plausible as sources of dust and gravel. But they also originate a whole long way further out. While there's a lot of mass in the Kuiper belt (possibly enough to match a small to medium sized planet, unlike the asteroid belt between Mars and Jupiter) the volume of space involved is vast—double-digit light-hours across. (One light-hour, the distance light travels in an hour, is 1.079x109km. Over a billion kilometers. If you set out to drive that distance in your SUV at highway speeds, it'd take you roughly 1150 years. Now multiply by a factor of 10-20.)
But basically unless your spaceship is parked on top of a frickin' comet approaching perihelion you are not going to get dust or gravel pinging off the hull ... unless you're insanely unlucky: because now the other shoe trops and we get to Annoying Trope #2.
Newton's Second Law, for dummies. E = 1/2 * (mv2) — it's not just a good idea, it's the law. Notice the huge distances I aluded to above? Well, to get between planet A and planet B in anything approximating reasonable human time spans, you need to go fast. And if you go fast, your velocity relative to the bodies around you is also high. In event of an inelastic collision the kinetic energy transfer is proprtional to the square of your velocity; and this has drastic consequences for space ships. Suppose you're in low Earth orbit and you hit a piece of space junk, for example a screw that's fallen off someone else's ship. It's traveling in pretty much the same orbit as you, but inclined at 30 degrees. What happens? What happens is you get a happy fun experience much like being hit by a bullet from a high-calibre sniper's rifle, because (I can't be bothered to do the trig here) it's packing a velocity component angled across your path at a goodly fraction of orbital velocity, and at orbital velocity a kilogram of water packs kinetic energy equal to about ten times its mass in exploding TNT.
You know what a high-speed car crash looks like, right? Space ships travel a lot faster than that: if they hit something, it's going to be very messy indeed. And that's at sluggish orbital velocities; if you starship is barreling along at about 85% of the speed of light general relativity has something to say on the subject and it's kinetic energy is equal to about half it's rest mass—the equivalent of a 10 megaton hydrogen bomb for every kilogram of hull weight. (The pilot's space-suited body alone packs the energetic punch of a Peak Strangelove 1980s USA/USSR strategic nuclear exchange.)
Human bodies are basically squishy sacks of goopy grease and water emulsions held together by hydrogen bonds and disulphide bridges between protein molecules and glommed onto some big lumps of high-grade chalk. We evolved in a forgiving, water-dominated low-velocity world where evolution didn't bequeath us nervous systems able to comprehend and deal with high energy interactions other than in an "ooh, that lightning bolt was close! Where's cousin Ugg?" kind of way. We can't even see objects that flash across our visual field in less than 50 milliseconds—a duration in which, at orbital velocity, an object will have travelled on the order of half a kilometer.
Intuition and high energy regimes: do the math, or your space combat will be a whole bundle of nope.
(Other related cognitive errors include but are not limited to: Napoleonic navies clashing in space and firing broadsides back and forth at one another's line of battle ... spaceships with continuous high acceleration fusion-powered motors or similar that don't glow white-hot then melt because vacuum is an insulator and shedding that much heat is a hard engineering problem (hint: a 100 ton spaceship accelerating at 1g requires 1 megaJoule of thrust: using a photon rocket for maximum efficiency that's going to require 3 x 1015 watts of juice going in, if it's 99.9% effective at heat dissipation that means it's racking up around three terawatt of leakage, and that's equivalent to about 45 kilotons of nuclear explosions per minute of waste heat) ... warships using active radar to hunt for one another (hint: active sensor reach is inversely proportional to the fourth power of the emission strength, passive sensors obey the inverse square law) ... warships using stealth in space (hint: infrared emissions, second hint: the background temperature you want to avoid standing out against is 2.73 degrees Kelvin, i.e. liquid Helium temperature) ...
Oh for fuck's sake, don't get me started on war in space, we'll be here forever unless we just throw physics to the winds of fiction and delegate all our hand-waving to magic hyperspace or cyberspace technology or something.
Now for a biggie: Mining the lunar regolith for Helium-3. This is junk science on stilts and it just keeps coming back from the dead. It's also a barrel of past-their-sell-by-date red herrings that keeps being rolled out by space cadets whenever they're challenged to produce an economic justification for space colonization. Here's why it's crap ...
Fusion, the Jenga-pile begins, is the energy source of the future. (This may or may not be true: I for one hope it is.) However, the easiest form of reaction you can run in a fusion power reactor is deuterium/tritium. This tends to release most of its energy in the form of neutrons, which can ideally be captured and used to breed more tritium fuel and produce waste heat to drive a turbine generator. The problem with neutrons is that they're rather penetrating and when they slow down enough to be captured by an atomic nucleus they transmute it, often into an unstable isotope. D/T reactors therefore look likely to suffer from one of the same problems as fission reactors: neutron-induced structural embrittlement and secondary activation producing high level radioactive waste.
Aneutronic fusion—which hasn't actually been tested yet in even a prototype research fusion reactor—offers the possibility of running on other fuels and producing <1% of its energy output in the shape of neutrons. Helium-3, an isotope of helium consisting of two protons and one neutron, can in principle be fused with deuterium instead of the (radioactive) tritium and produce power with a far lower neutron output—the energy-bearing product of the reaction is a proton, which can be contained using magnetic fields. Hence the interest in He3 fusion reaction designs.
The first problem with He3 reactors (after—cough—we don't know how to build one yet) is that He3 is incredibly rare. It costs on the order of millions of dollars per kilogram and the global supply is very restricted; there's certainly not enough of it to power a global energy economy even at today's levels. But there is some evidence that He-3 produced in the sun and emitted in the solar wind may be captured in the Lunar regolith. The plan, per the proponents of lunar colonization, is therefore to build vast strip mines on the moon to extract this vanishingly rare moonshine/pixie dust and export it to Earth to power our 22nd century energy economy. And of course estimates that we could power our current level of energy use by processing 4 million tons of lunar regolith per week are music to the space cadets' ears because, well, it means big engineering and thus big steely-jawed engineers with slide rules and socket wrenches on hand to repair the mining machines when they break. Space colony justified!
Except this is moonshine and junk. Firstly, we don't have an aneutronic fusion reactor, much less a planetary base load capacity driven by aneutronic fusion reactors in need of fuel. Hell, we don't even have a working D-T fusion reactor that can produce surplus energy; ITER isn't due to achieve first plasma until 2020 and won't begin D-T reaction operations before 2027, and the Wendelstein 7-X, while promising, is a generation behind (roughly equivalent to where the Joint European Torus was in the 80's).
But let's jump the gun. Let's assume we do have a working fusion reactor. Let's even assume we've put in the decades of legwork required to build a working aneutronic fusion reactor—it's worth noting that aneutronic reactions have to run about an order of magnitude hotter than D-T fusion reactors can achieve, and they're already in the 100 million Kelvin range. But let's play make-believe: are we then going to see large-scale lunar regolith mining to fuel the beasts?
Because it turns out that if you can build an aneutronic reactor, then, subject to some considerable amount of fine tuning, you can run it on fuels other than sparkly lunar regolith moonshine and pixie dust—notably the proton-boron-11 cycle and the proton-lithium-7 cycle. Both these fuel cycles are aneutronic and run on isotopes that are readily available here on Earth in sufficient quantities to power our civilization for some millions of years without trying to build massive engineering infrastructure on an airless rock. There's even an aneutronic fusion cycle that relies on proton-nitrogen fusion, although it produces less energy and is even harder to achieve. Nitrogen and hydrogen ... nitrogen makes up about 80% of our atmosphere, and hydrogen makes up about 15% of our hydrosphere, so we're not running out of either of those fuels any time soon, either.
Upshot: any work of SF that takes "Lunar 3He mining" as an economic premise is about as plausible as one that assumes combustion powered by the release of phlogiston.
I've got a whole bundle more shibboleths up my sleeve that flag a work of SF as being implausible (this may account for why I'm more comfortable reading fantasy these days). Faceless 80's style corporations ruling entire planets (hint: who handles the externalities?): small farming planets (hint: just one ecosystem for a planet?): the glib dismissal of life support systems in space as trivially easy to maintain: monocultures of every kind: political structures based on design patterns proven to be unworkable in the context of any society more modern than the late middle ages (empires in space, I'm looking at you): any interplanetary/interstellar setting where the mechanics of trade are lifted straight out of a Joseph Conrad novel, or 1920s era pulps about life aboard a tramp steamer, or maybe the Traveller role playing game: AIs that follow the disembodied-brain-in-a-box mode of Hal 9000: futures in which we wear mini-dresses and three-piece suits, drive gas-burning automobiles (or hovercars: it's just a rabbit/smeerp replacement), carry handguns (or blasters: see rabbit/smeerp), eat the kind of food we eat today, live the kind of way we live today, and most importantly think the way we think today.
And I haven't even gotten as far as genre fantasy shibboliths yet!
So, over to you: what do you stub your toes on when you read SF, that throws you out of the state of willing suspension of disbelief?
Edit: if there's an entry for your pet shibboleth in the Turkey City Lexicon don't bother repeating it here—I'm taking familiarity with the canonical list of cliches as a given.