Plot hole: In this movie Goblin was able to sneak up on Peter. But in the previous movies Peter was able to sense danger from quite a distance away; Green Goblin from a few blocks and the train barricade from over a mile.
Plot hole: At the end, none of the duplicate Benders that are waiting in the limestone cavern under the Planet Express building have had their Obedience Virus or the time code deleted from them. There should have been only one Bender without the Obedience Virus, not all of them.
Plot hole: When Wilbur and Lewis are time traveling for the first time, Lewis says he's done with the memory scanner. Since he said he wouldn't invent Dor-15, and she went away, wouldn't the time machine and everything else in the future go away since the memory scanner started it all and Lewis decided to quit?
Suggested correction: Lewis wasn't fully giving up. He was just frustrated and probably went back to it later anyway. Whereas with Doris, he deliberately decided not to invent her because of the danger she posed.
Plot hole: I can somewhat understand that in a kiddies' show all aliens can inexplicably speak English - but using Terranean (i.e.: Arabian) numbers as well? While Tetrax's computer uses alien runes, the readout on Gluto's holographic HUDs use Arabic numbers - somewhat a bit too deliberate a producer choice to emphasize intergalactic communication.