Rez says the reason they found Juni on level one was that François was caught cheating in the mega race. However, when the boys get to the mega race in Level 2, a character says that there are no rules in the mega race.
Near the end of the movie, Carmen tells Romero that they only have one pair of glasses left. This can't be true, as Carmen gives Gary glasses when he arrives and Gerti is also wearing glasses, so we can assume that Juni gave them to her.
After the group falls into the "lava," Carmen is signaling Juni where to go. She's holding her breath at first, then smiles at Juni, which would release all the air she was holding. She then goes back to "holding her breath."
When Gerty and Juni are talking in the tree house, Gerty is drinking a cup of apple juice. When she is done, she wipes her mouth with a green napkin and puts it down. In the next shot, the napkin is still on her mouth and she puts the napkin down for the second time.
At the end of the movie, when Dinky Winks waves his branding iron at the camera, it spells D-I-N-K-Y. This means that his name would end up branded onto the robot backwards--if it's even possible to brand a robot, of course.
Right before the "mega race" starts, one of the "beta tester" kids turns around to the audience as if he were addressing Juni and says "we'll try to help you out as much as we can" but the vehicle that Juni is driving is clearly visible in front of him as he says it.