I'm going through the TOS films at the minute. Just finished Search for Spock actually.
In TWOK only thing that got me was Chekov mentioning the things in the ear and McCoy totally ignoring it.
However, SFS has quite a few. Not the Excelsior stuttering to a halt. The fact it's engine's conking out sound like a real world car is pretty stupid, but the physic, well the films seem to treat spaceships like planes - except for the 3D thinking (which is perfectly for to me) - with slow turning angles etc, so I'll excuse that one.
However, the Enterprise arriving at the Genesis Planet, sees no ships because the Klingon Bird of Prey was cloaked. What about the Grissom's wreckage? That'd have been a nice little nod to have Kirk on edge, which wouldn't have hurt.
Then there's a few technology ones, Kruge teleports up while the ship is cloaked, photon torpedoes seem to act more like Star Wars Ion cannons than the destructive power of photons we've seen everywhere else. Enterprise's self destruct acts like explosives are ringing the ship, which is a rather terrible design decision. Surely it'd just be warp core exploding. But the engine's are completely intact. It's the saucer section that explodes.