In the scene where Shinji is with Kaji in the garden of watermelons, Shinji and Kaji don't keep the same position, every camera angle place them in different positions. In the first shots, there is a small dirt path between the two characters, but in subsequent shots, there is no path. And in the same scene, Kaji has dirt stains on his face, which change position between shots.
Misato is referred to as a Colonel in dialogue, but her rank is displayed as Major in "on-screen" text in at least two scenes.
Azuka is cooking, in the scene there is a pot on the stove, Misato comes to see what happens, from the Misato's POV, Azuka is holding the pot, but in the next shot, the pot is in the same position.
In the first scene, Kaji talks in English with other European Union members, but the voice is completely different when he talks in Japanese.
Mari is supposed to be British, but in the scene where she speaks in English, the accent is American.
The Angel Zeruel manages to blast through every layer of armor above the GeoFront. In the English dub Hyuga says that there are 27 layers, while in the Japanese dub he says that there are 24 layers (as indicated by the on-screen display).