Factual error: When Gwen and Grandpa Max use the shell plates from the tick to ward off it's corrosive secretions, their fingers should have been eaten away since they were grabbing the rims of the plates when the acid came raining down.

Continuity: 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: 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.

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".

Continuity: 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.

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.

Factual error: It would be highly impropable 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.

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.