These are just in the order that I think of them....
1) the explanation for how Kitty Pride was able to send people's brains back in time was non-existent. On top of that, the explanation for why Wolverine had to be the one to go back in time was so lame and glossed over, it was painful. His brain synapses would regrow. But we never showed the process as being painful... it was a lame excuse to make sure that Wolverine was front and center again.
2) At the beginning of the Vietnam War, Logan is a soldier and is recruited by Col. William Stryker. But now, at the end of the Vietnam War, Logan is not, and Major William Stryker meets him for the first time?
3) When in the conference room, and Wolverine goes nuts because he sees Stryker, we see Future Wolverine pop his claws. He flails around in the future, even stabbing Kitty. Then, when Past Wolverine gets his crap together again, Future Wolverine retracts his claws. So, clearly, Past Wolverine and Future Wolverine are co-existing in real time. This means that Kitty, with her gut stabbed a foot deep with adamantium... thrice... and nothing but field dressing on the wound, held Wolverine in the past for a flight from Paris to New York, a come-to-Jesus in Westchester, a joint chiefs + advisers meeting, and the planning and execution of a huge press conference in which 50 different countries sent cameras. We see Wolverine take a nap, I'm pretty sure. At the most conservative estimate, this whole process will take, likely, a week. She would be septic and dead long before Wolverine got home from Paris.
4) the way they treated Quicksilver's powers, he's pretty much a fix-any-problem mutant. Why do they leave him home? They want to keep Mystique from killing Trask? What about the dude who has shown that a room full of shooting people shooting was no problem did they decide wasn't up to the task? Are you gonna tell me that he was too young to involve in the further situation? Old enough to break into the Pentagon, not old enough to... prevent the assassination of a dude on the other side of the world? And for that matter, when everything was going on on TV, why was he just sitting there like a jackhole without super speed? The Quicksilver we met would have been in Paris in 5 seconds, or at least in DC in less than 1. What part of the dude who stole a security guard's hat while dealing with all the bullets wouldn't be an asset going into a potential fight with a dude wearing a hat that makes Xavier's power's useless?
5) Blink + Colossus + Warpath = awesome. Can I have a movie of those three beating up, I don't know.. Nazi's or terrorists or something?
6) Eric killed JFK, or at least the U.S. Government is convinced enough that he did that they built a cell for him in the courtyard of the Pentagon. Keep in mind that this takes place before anything from the past changes. He's a Presidential Assassin. How does he end up just chillin' in a Senate Hearing in X1?
7) Speaking of Eric in prison, the courtyard of the Pentagon is 5 acres large. A regulation baseball field is 3 acres from backstop to radial arc. We know that Eric was able to activate the Sentinels from inside a baseball stadium at least a baseball diamond + outdoor park + highway away, meaning his power extended much further than 5 acres. was Magneto hanging out in prison because of 3 squares and alone time to catch up on his reading?
8) Speaking of the Sentinels. We're in a post JFK assassination world. The Secret Service would have every inch of the agenda for the announcement of the Sentinel Program. They would know who was speaking when, when the band was going to play, and every other detail. When those giant purple robots turned on, when they weren't supposed to, they wouldn't have just stood there, the President would be on his way to the bunker. And they certainly wouldn't have put him in the same bunker as the only person they believe has the ability to turn on the flying death machines that just started shooting people.
9) Speaking of the giant purple robots, when did it become part of Basic Training to teach members of the military to salute giant purple robots? the minute that sheet dropped, every person in uniform at the event stood and started saluting. The robots. Their salutes followed the robots up into the sky when they took off.
10) speaking of the sheet keeping them hidden, what was with the President of the United States standing in front of a United States of Trask Industries flag? That was just weird....