Be Afraid of the Dark (2) - S3-E12
Plot hole: When the Corrodium Beam is shut down, there is a brief scene of the sky clearing at Mount Rushmore. But on the cliff face all four heads are seen, whereas the head of Theodore Roosevelt got crumbled in "Secrets," and it's too far forward to have been carved into the mountain face, in place (and same position) of the old head, yet again.
The Alliance - S1-E8
Plot hole: After Upgrade has successfully removed Rojo's cybernetic parts, the beam rifle she had used in the armoured car heist at the episode's start suddenly appears among them. But when the drone merged with her, she wasn't holding the gun and so it couldn't have been transformed along with her.
Plot hole: In Ben's nightmare, Gwen says, "We will come and get you!" and then she nags at Ben for being the one with the alien powers, and she does not join him in climbing the tree. My guess is that this was due to a script error; it was likely supposed to be "he" (i.e. Ben) instead of "we".
Lucky Girl - S1-E10
Plot hole: When Hex revives in the ambulance, the stone to the right of the glowing Reincarnation Charm is the Luck Charm - which Gwen has at that time. Therefore it should be missing from the necklace, but there it is.
Back With a Vengeance - S2-E13
Plot hole: It is rather strange that grandpa Max would have a kid-sized Plumber suit ready for Gwen, given a) that the Plumbers are effectively defunct, and b) that a government organization would hardly allow underage trainees in their ranks.
Plot hole: The alien mummy is found by the werewolf in a separate rectangular block of concrete. However, I don't think that the Tennysons would have made the effort of first enclosing the mummy in a separate load of concrete, waiting until the stuff is hard, then putting it into the hole and covering it with a new load of concrete. Too much effort and too little time for one night ("Under Wraps"), since concrete does take time to get hard properly.
Plot hole: When the mutated sea gull attacks the Tennyson's' sailing boat, it brings down the sail. But then the piece from under which Ben and Gwen emerge suddenly has a convenient wooden lattice fixed to it, whereas in reality it should have none.
Ben 10 vs. The Negative 10: Part 2 - S4-E9
Plot hole: Rojo (from first season's "The Alliance") makes her second appearance in the series in a suit of powered armor. However, in "The Alliance" she had been turned into a cyborg by Vilgax' drone and thus looked radically different than she does here. So how can Max say: "How did she get back her alien tech?" when her equipment and weaponry was totally different in their first encounter?