The Origin of the Fantastic Four: Part 1 - S1-E1
Other mistake: When Puppet Master is making a clay figurine of Thing, the mold he uses doesn't have a Thing-shaped interior with which to make a detailed figurine. The figurine should have just looked like an undefined human-shaped figure. (00:15:20)
Other mistake: Despite being in the same continuity as the 1992 X-Men animated series, this show depicts Bill Clinton as President of the United States, while in X-Men, the President is Robert Kelly.
The Return of Hydro-Man: Part 1 - S5-E7
Other mistake: When Spider-Man catches up to Mary Jane and Hydro-Man at the foundry, he webs up Hydro-Man's left wrist. When the shot changes to Spider-Man landing, he is not holding onto the web-line. When the shot changes back to Hydro-Man, his arm his pulled with the web-line remaining taut, even though Spider-Man is not holding the web. If Hydro-Man was moving his arm on his own, then the web-line would be slack.