The Big Tick - S2-E2
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.
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.
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.
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.
