Continuity mistake: Season 4, episode 10 "Ben 10 vs. The Negative 10, Part 2": When the Forever King makes his announcement "Nothing will stop this little home-coming", he stands outside the Mount Rushmore base on bare soil. But in the scene where Max reviews the recording of this speech, all of a sudden we find the Forever King standing on a neatly tiled floor.
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.
The Krakken - S1-E3
Continuity mistake: When The Krakken snatches the Cannery crate from the boat, you can see that the lower horizontal bar from the 'E' is suddenly missing, thus reading 'Cannfry'.
Revealing mistake: It is strange that the news coverage at the beginning of this episode is able to cover the story from all angles in such rapid succession: from the helicopter straight to the ground, then even a close-up of the goon atop the crystal mount Diamondhead traps him on.
The Krakken - S1-E3
Continuity mistake: When Ben pretends to be sucked into the lake, and Gwen turns around to look after him saying "I'm not falling for it", she's missing her eyebrows for a second or two.
The Alliance - S1-E8
Continuity mistake: When Rojo attacks the police academy, there is a patrol car right behind her. But when Ben (as XLR8) arrives and slams into her, the car suddenly vanishes.
Continuity mistake: Season 4, episode 9 "Ben 10 vs. The Negative 10, Part 1": When Charmcaster waves her good-bye to Gwen just before Animo swoops her up, the coloration of her waving sleeve's decor suddenly changes from violet to purple.
Continuity mistake: When the Tennyson's RV passes by Rapid City when it comes under attack by Vilgax, it's the first time the outskirts can be seen. But later, when the gas station explodes, the entire town is suddenly hidden behind a mountain range.
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.
Continuity mistake: The number of rockets Sixsix has on his wrist launcher alternates between three and four, especially during the final combat scenes.
Revealing mistake: Season 4, episode 5 "Ben 4 Good Buddy": When the Baron drives off from the garage in the Rust Bucket, the VR's interior shifts unnaturally; an obvious glitch in the computer animation.
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.
Deliberate mistake: When Sixsix impacts with the ground due to Greymatter sabotaging his jet pack, the furrow he ploughs into the ground is already present when he skips across the ground.
The Alliance - S1-E8
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: 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 mistake: When the Marty-alien removes the dumpster as Ben watches him, there is a set of stairs leading down. But later, when Ben (as Wildmutt) and Gwen jump down the shaft, the stairs are gone and there is an iron ladder.
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.
Continuity mistake: When Ben is upset because he is too short to go on the water slide, he is wearing a bathing suit. But in the shot where the Omnitrix deactivates and he is back to being a human, he is in his normal uniform.
Continuity mistake: When the three old people throw the car at Ben and Gwen, Ben doesn't have the Omnitrix on for a few seconds. (00:14:10)
Lucky Girl - S1-E10
Plot hole: When Hex revives in the ambulance, the stone to the right of the glowing Reincarnation Charm is the Luck Charm - which Gwen has at that time. Therefore it should be missing from the necklace, but there it is.