Yeah, I figured the same thing about the "cure" only being temporary. I also think it has something to do with the level of the mutant and how many darts were used on them or how much they were injected with.
The only major mutants that got "cured" and survived through the end of the movie were Magneto, Mystique, and Rogue. Magneto got 4 darts, Mystique got 1, and Rogue was injected with however much. And by the end of the movie, Magneto started to get his powers back. So if Magneto's a level 4 and he got injected with 4 darts and he was able to start using his power by the end of the movie, then Mystique, who's about a class 4 should have her full powers back before Magneto. As far as Rogue, she'll be in the middle of doing Bobby and her powers will suddenly come back and she'll end up killing him.

lol Rogue, in my opinion is about a class 2 at most. Now in the cartoon and comics she's about a 4, but unfortunately she hasn't been blessed with those other powers in the movies (which really sucks!).
I had another theory that either some mutant tampered with the cure or Apocolypse killed Angel's father, took his form and messed with the cure and made it make the mutants more powerful (not right away, but over time). Then Rogue would end up with all her powers. Cause let's face it, the chances that the movie people are going to go with the sucking of Ms. Marvel's powers probably isn't going to happen. This would give them a way out possibly. But that wouldn't really work, cause why would Apocolypse want to make any mutants more powerful? For my theory, it's just a way to make Angel hate Apocolypse like he does in the cartoon and comics.