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 Nudar first uses the time sphere, he has to say "Yesterday" to go back in time. Yet whenever Bender goes back in time, he doesn't have to say anything.
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Suggested correction: If you notice when Nudar was in the time sphere, time around the sphere seemed to slow down, so Bender could have just been faster than everyone else as he was stating the time he wanted to go to.
