Videogame nitpick:
It always bothers me that during the ending of Final Fantasy 7, when the camera swoops down to the city to focus on the little girl, you can clearly tell the entire backdrop is just a flat silhouette. Since most of the game uses prerendered backgrounds, with a top down perspective you would never see this detail. But they used the same model for the cutscene, which painfully puts this shortcut on display.
FF7 Ending (spoiler!)
Movie nitpick:
How come the Gremlins can drink beer, which clearly contains water, without multiplying? Or run through the snow? How come they can watch a movie in a pitch black theater, without reacting to the bright light? I know Gremlins 2 pokes fun at plenty of other silly things, so I probably shouldn't think too hard about these things.