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 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.
Deliberate mistake: When the Tennysons drive towards the city's power plant, Grandpa Max is using the left side of the highway instead of the right. Even with a looming nuclear accident, correct traffic habits do play a role, especially on such a narrow highway. Who knows whether one might drive down the road in a hurry and you approach him on his side of the highway?
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: 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.
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.
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.
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.
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.
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 Krakken - S1-E3
Audio problem: When the kraken roars, when it destroys a ship, it sounds like a TIE fighter in Star Wars.
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.
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.
Other mistake: When the Tennysons drive towards the city's power plant, Grandpa Max is using the left side of the highway. Curious, since you drive on the right in the USA - regardless of the looming nuclear accident there was no reason to invite a crash like that.
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
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?
Continuity mistake: Season 4, episode 9 "Ben 10 vs. The Negative 10, Part 1": When Charmcaster taunts Gwen about not having "taken off the training wheels", she moves her head upward. Note that the lower part of her ponytail falling over her backside does not move as the upper part does, but remains fixed in place.
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)
Other mistake: In Ben's dream, Wildmutt's brace is the same color as his body while Ghostfreak grabs him.