I've got a few that annoy me. I'll spare you the obvious tropes (token black guy ALWAYS dies first, etc.)since those are "no shit" type answers.
Now, as an amateur filmmaker, I work with special effects, both digital and practical on a semi-regular basis, so bad special effects stand out. No, I'm not talking about the hilariously and easily spotted fakeness like Birdemic's birds. No, right now I'm going to use the movie Skyline as an example. My friend and I found ourselves really pissed at a certain scene in the movie, where an atom bomb goes off about half a block down from the main characters' apartment, and it winds up getting it all wrong from a physics standpoint. Now if you know anything about explosives, you'll know that in addition to the blast of fire and smoke, there's a kinetic shockwave of sorts that demolishes and repels any object in the blast radius. The bigger the bomb, the bigger the shockwave. The bomb in skyline was easily a nice big one that could level a couple blocks. In the film however, it doesn't do shit towards anything outside the initial firey blast. I man, for fuck's sake, at least knock down the characters. You know what did this right? Mass Effect 3. In the beginning a reaper destroys a human ship in a catastrophic explosion that knocks Shep down and knocks out the girder they stand on through sheer kinetic force. That's how you do it right.
On a side note: SEE? I CAN SAY NICE THINGS ABOUT MASS EFFECT 3!