Plot hole: Vanessa seems upset at Barry when their actions at getting the honey back from the humans result in the flowers and other plants dying. One might think that Vanessa, as a florist, would know the outcome and would warn Barry instead of helping him with his plan. Yet she appears to blame him for the entire outcome when it becomes apparent.
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: There are two cars driving behind the EPA truck containing Marge, Bart, Lisa and Maggie. When Homer uses the bulldozer to try and break the family out of the truck, the two cars behind the truck don't notice the bulldozer trying to destroy the truck. There's no way they couldn't have not seen the bulldozer since they were just behind it. (01:00:05 - 01:00:40)
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.