When Electro is telling the Caped Crusader his plan while holding them both in one hand, in one shot, the reflection on the vehicle's window is layered over Batman and Robin instead of behind them (animation cel layering mistake).
At the start of the story, Batman and Robin are seen working on the Batmobile. When Robin is standing over the hood, a view from his backside is seen, and his cape is green. When the shot changes to a front view, his cape is yellow, which is the correct color.
When the shrunken Batman stands next to a mop and pail, he is drawn wearing an eye mask like Robin's. Possibly the animators forgot to "color in" Batman's cowl forehead, leaving it skin-colored.
Before landing in the desert, the Commander tells Electro that there is no civilization within 100 miles of them, yet when the ship lands, you can see what appears to be a city only a few miles away.