Back by popular demand! 
Don't worry, this is the last one
1) At the end of the movie, Kirk gets promoted from "cadet" all the way to "captain". WTF? Sure, he defeated Nero (mostly due to luck), but how does one day of heroics make up for years of experience? How many times did Wesley Crusher save the Enterprise only to receive nothing more than a pat on the back and a "good job Ensign, now get back to your post"?
2) In the final action scene where Kirk beams aboard the Narada to fight the Romulans, how is Kirk able to move at all? He seems miraculously agile for someone who has, all in one day, A) suffered a severe reaction to a vaccine against Luvaran mud fleas, B) gotten his ass kicked by the Romulan on the drilling platform, C) Gotten Vulcan-death-gripped by nuSpock, D) trekked 14km through a frozen wasteland on Delta Vega, and E) Gotten his ass kicked (and nearly choked to death) by Spock when he gets back to the Enterprise. Despite all this, he's able to move around quickly and freely as if nothing has happened to him at all.
3) Why the hell don't they use the red matter to create a black hole, go back in time to 5 minutes before Nero appeared, and ambush him? Wouldn't that negate everything Nero did, and all the people he killed?
4) When Kirk, Sulu, and Olson parachute down to the drilling platform, Olson is carrying the charges, but gets vaporized by flying into the drill laser. Shouldn't there have been a massive explosion when this happens, as all the charges blow up?
Don't worry, this is the last one
1) At the end of the movie, Kirk gets promoted from "cadet" all the way to "captain". WTF? Sure, he defeated Nero (mostly due to luck), but how does one day of heroics make up for years of experience? How many times did Wesley Crusher save the Enterprise only to receive nothing more than a pat on the back and a "good job Ensign, now get back to your post"?
2) In the final action scene where Kirk beams aboard the Narada to fight the Romulans, how is Kirk able to move at all? He seems miraculously agile for someone who has, all in one day, A) suffered a severe reaction to a vaccine against Luvaran mud fleas, B) gotten his ass kicked by the Romulan on the drilling platform, C) Gotten Vulcan-death-gripped by nuSpock, D) trekked 14km through a frozen wasteland on Delta Vega, and E) Gotten his ass kicked (and nearly choked to death) by Spock when he gets back to the Enterprise. Despite all this, he's able to move around quickly and freely as if nothing has happened to him at all.
3) Why the hell don't they use the red matter to create a black hole, go back in time to 5 minutes before Nero appeared, and ambush him? Wouldn't that negate everything Nero did, and all the people he killed?
4) When Kirk, Sulu, and Olson parachute down to the drilling platform, Olson is carrying the charges, but gets vaporized by flying into the drill laser. Shouldn't there have been a massive explosion when this happens, as all the charges blow up?
