I might say "Back to the Future", but, I'm not sure I can really consider it quite the same, since it's more how it dragged on, rather than how it ended.
I noticed recently that an old childhood game of mine called "Frogger 2: Swampy's Revenge" had kind of an irritating ending. Frogger and Lillie Frog are still stuck in that cage! How do they get out? On top of that, Tad's escape kind of rendered all previous events of the entire game totally pointless. Not to mention how Swampy's machine blowing up somehow makes the sun come up instantly, complete with chirping birds. I suppose Zapper: One Wicked Cricket made up for that. Very overlooked game. I absolutely adored the ending in that one.
Oh... Sonic Generations. For so many reasons. Namely, because both Sonic and Eggman created their own boostrap paradoxes. And how so much of it just doesn't make any sense. The paradoxes are probably even worse than '06. Then again, the story wasn't good to begin with, but, come on!
Then, there was this one film... Can't remember what it was called, though. Some nerdy gamer kid was being picked on so bad, but some girl he met in an RPG was trying to help him through it. Then, he faked a suicide to try and make a point. Well, that's all well and good, except that it's revealed that the girl was a figment of his imagination the entire time! Thus, creating one huge paradox! How could he have learned all of these things from her if she never existed? How can his brain teach him things he didn't even know? How could those bullies have picked on him drugged as their reaction to the message he got from her on his cell phone? Why would he get on the train with her if she wasn't real!? It just seemed to ruin everything the film was building up and standing for.
Good grief, I wish I could remember the name of that movie. I think it was like "Something X" or something or other...