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.
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".
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: 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: 4-9 "Ben 10 vs. the Negative 10 (Part 1)": 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?