Starships meeting each other in the same plane and the same way up as if they're sailing on an ocean, rather than travelling through a frictionless 3-dimensional space.
Ships always travelling with the "front" facing forwards, rather than sideways, backwards, upside down, etc.
"Fighter planes" in space, especially when they swoop around, banking to turn as if they're travelling in air. Babylon 5 made an attempt to get this right, when a fighter turned round on its own axis whilst still continuing to travel in its original direction, so it could shoot at an enemy on its tail. Makes a mockery of all those "he's on my tail, I can't shake him off" scenes in things like Star Wars.
Space battles in general, especially in Deep Space 9. Where capital battleships have to fly right past each other firing broadsides like they're warships of the Nelson era - rather than sitting back out of visual range of their enemy and using guided missiles to attack them, as indeed real naval warfare does today.
Asteroid fields in things like Star Trek and Star Wars being huge jumbles of rocks swirling around each other at ridiculous velocities making them hazards to navigation - rather than say being mostly made up of empty space with an asteroid every few thousand kilometres, like in the real asteroid belt.
Alien civilizations all being humanoid I can live with - what bugs me is when they're all at roughly the same level of social and technological development, as if they all evolved at the same time and at the same rate - there's such a narrow window of time for these things to happen, in the vast and infinite universe, it's quite implausible that you have so many at comparable levels. That's one reason why we'll probably never meet aliens - because another civilization won't rise during the time that humanity exists. Either they've already been and gone (we might find their artefacts), or they've yet to evolve.
All these things bother my science head, and yet I can still enjoy the shows in question. My favourite outer space show though is Space: 1999, which has a much more intelligent and challenging grasp of science.
