When the ship is crashing, Fry screams "We've lost power in the forward Game Boy! Mario not responding!", but it is seen he is holding a NES controller. There are SUPER GAMEBOY systems for SNES and N64, but not the NES, making that option irrelevant.
When Bender is crawling out of the Cyclops-eater's mouth, he's briefly shown with his two eyes, while he's supposed to have only one. In the next scene he only has one eye again, putting his second eye back in.
During the final scenes where the Leela-Bot says "Let's ditch these meatbags!" and sheds her skin, the Wrist LoJack-a-mater (which the real Leela wears) appears and disappears on her right wrist in the same shot.
In the last scene the Professor and Fry effortlessly lift Bender up in celebration, which is an amazing feat considering he weighs 525 pounds.
How could the Professor use the Sphere-O-Boom to save Bender when it was already destroyed in "Bender's Big Score"? The answer could be that the professor had a spare one locked in which the nudist alien scammers could not get to it
The Leela-bot's original looks (before using the artificial skin) and it's looks after it sheds it's skin don't match.