Continuity mistake: Fourarms Gwen launches four bowling balls with all her arms at the same time, but the balls strike the pin sets one at a time.
The Galactic Enforcers - S2-E6
Other mistake: Generally, voice actors are listed only by the roles which they actually perform in the respective episodes. Even though Ripjaw's voice, Fred Tatasciore, voices Cannonbolt and others throughout the series, the character of Ripjaws does not appear in "Galactic Enforcers" and thus should not be listed in the credits.
The Galactic Enforcers - S2-E6
Other mistake: In the end credits, one of the characters listed is Ripjaws, who is, however, actually not featured in this episode.
Continuity mistake: When grandpa Max first wakes up in the fungi cave, we find him completely wrapped in tendrils. But when XLR8 comes to cut him loose, Max' shoulders are suddenly free.
Other mistake: Gilbert is the only one to have a name tag, whereas Andy and Mandy don't - rather strange for a summer camp where dozens of kids tend to run around to issue tags to only some of them.
Factual error: When Enoch is seen with the dust which has once been the sword, there is a larger dust pile than the sword blade would have left on the floor.
Other mistake: Grey Matter held his breath underwater to save the drowning man, but he has gills so that he can breathe just like fish.
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".
Factual error: When Ghostfreak first escapes the omnitrix, right before he rips off his outer layer of skin, he still has the omnitrix logo on him even though it should be gone with him being outside the watch.
Continuity mistake: When Ben, Gwen and Max try to track down Ghostfreak, Max's scanner picks up "trace spectral activity from around that corner", which happens to be right ahead, but then Ghostfreak and cohorts appear from behind. In a deleted scene featured on the series' DVD, the source of the reading is revealed to be the tuba player Ghostfreak had possessed, who instantly runs off at the sight of Fourarms.
Other mistake: In Ben's dream, Wildmutt's brace is the same color as his body while Ghostfreak grabs him.
Back With a Vengeance - S2-E13
Factual error: It would be highly improbable for Kevin to find Vilgax frozen deep in space. As we see in first season's episode 'Secrets', Vilgax's ship was blasted apart in the upper atmosphere - after all, Ben escaped as Heatblast, and he wouldn't have been able to once beyond the stratosphere. Earth's gravitational pull would have kept Vilgax on Earth, not released him into deep space.
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.
Continuity mistake: As grey matter is running to avoid being smashed by presents he isn't seen till he randomly appears on the second present. (00:17:45)
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.
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.
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.
Other mistake: In the voice cast list, the Groom's Father appears twice - with two different voice actors - and the Groom's Mother is not even listed.
Continuity mistake: The priest who presides over the wedding gets a faceful of muck by the bride's parents. When he flees the scene, screaming, he is peachy-clean, but later, as the ceremony is happily concluded, he suddenly has muck stains on his head and robe.
Ben 10 vs. The Negative 10: Part 2 - S4-E9
Continuity mistake: As we could see in first season's final episode, "Secrets", Roosevelt's head on Mt. Rushmore was totally destroyed, and in most subsequent episodes - including this one's first part - there is a sizable hole in its place. But after Ben asks whether the plumbers' hologram technology can replicate 'big presidents', and the scene changes to the demolished presidents' heads, the crown of Roosevelt's head suddenly joins the others on the mountainside.