1. No Sound in Space
As space is a near vacuum their is no sound. That means so engine noises, explosions, etc Very few movies and games get this right.
2. Spacecraft Do Not Fly Like Aircraft in an Atmosphere
See point 1. Furthermore they shouldn't move in space like aircraft, submarines, etc. For every action there¹ is an equal and opposite reaction. This also means your spaceship will not have a top speed, essentially, as if you have thrust, you have acceleration, and your speed climbs. However at some point you'll have to arrest that momentum.
I say "essentially" as space is a "near" vacuum, some atoms of this or that do exist, as do dust particles and larger. Eventually, and that eventually may be millions of years into the future, the object may encounter enough "stuff" that the motion of that object is significantly slowed. Or of course it travels a few kilometres, and is pancaked by a large asteroid in its path.
As an example for Eve Online. If my ship is moving, and I jettison a can, that can should continue moving through space forever at the same speed of ejection and in the direction it was ejected.
Realistically the game engine cannot be expected to track millions upon millions of objects forever, but perhaps until downtime, or even an hour, would be possible.
3. No "Hollywood Helmets"
When you're in the dark, trying to be all stealthy, the absolute worst thing for you are lights shining in your eyes, illuminating your face for the bad guys and ruining your night vision. That is what a "Hollywood Helmet" is. You'll see them in many Sci Fi movies, and probably some games. The reason they do it is simple, it shows the overpaid actors face, stroking their ego just that little bit closer towards completion. If I was the bad guy though, I'd be super stoked the people I was trying to kill gave me a perfect target location, all lit up, that would also be an almost guaranteed kill shot.
4. Everything is Moving!
I've touched on this before on this blog, and also above, but in space everything is moving. I'm standing on a planet rotating on its axis, which is orbiting the Sun, the Sun is orbiting the centre of the Milky Way, the Milky Way is moving in a direction with other galaxies in The Local Group, etc etc. Everything is moving. So why isn't everything moving in Eve Online? Partially it's because Eve is an old game at its core, and having everything moving back in the day would have not been technically possible. These days it may still not be but more objects could be in motion than they currently are. Bookmarks wouldn't have to be different from now, as they would also move in relation to whatever object was closest. Using the Earth year as an example (which would be atypical in reality Universe wide) you should be able to visit a planet in Eve over the course of one year and the location of the planets, stations, citadels etc in that system would change due to their orbital mechanics. This wouldn't change the game mechanics, but it would look more realistic.
Where it would change the game is missions, PVP, objects, etc. An example. A ship is destroyed and drops several containers which are ejected at 2000 meters per second in random directions. They keep moving, they're getting away, which ones do you chase?
Annoying? Yes. More realistic? Also yes.
5. Space Doesn't Have Shock Waves
Well in fact it does, but only when matter is encountered. This is seen quite clearly around stars which have exploded for one reason or another. If a missile explodes in Eve Online their should be zero shock wave, as their is essentially no gas to compress. However the particles of the missile, casing, shrapnel, etc would continue outwards striking everything in their way, essentially forever.
Another bloody quarry/old factory. You'll see this one, from my experience, more in older British Sci Fi, but the amount of episodes that just get lazy or cannot afford decent locations is tiresome.
Where do I start? Budget reasons cause most of the following problems, but some would not be hard to avoid.
Aliens are not human shaped with funny ears and/or noses.
Some aliens should breathe other gases and/or liquids than oxygen.
English is not the universal language, in fact it may not even be our semi-universal language. These stories are often set a few hundred years in the future. Consider how much English has changed in the past few hundred years, the changes now we are seeing with a new type of shorthand thanks to mobile phones and online chat programs, now extrapolate all of that into the future. However with the introduction of the internet, and the equivalent of the internet in the distant future, that may in fact be homogenising the language towards something more stable.
But that probably isn't English as we know it.
Translators are fine, in the ear, on a device, whatever, but then the mouth movements shouldn't match the translated language should they?
Inter species sex. Where do I put it? Can I put in somewhere? Is that how you do it? Do you rip it off afterwards? Does the place I'm about to put it into have thousands of rotating grinding little teeth?
Talking before intimacy will never be more important.
Earth standard gravity is not universal. Again this is usually done for budget reasons but as we've found the mass of our planet Earth is not common, and so therefore our amount of average gravity shouldn't be either.
¹ I'm aware of the grammar error, but I'm uneasy correcting Newton.