The Return of Hydro-Man: Part 1 - S5-E7
Continuity mistake: When Spider-Man is in the lab analyzing Mary Jane's jacket for clues, the inside of the door to to the lab has the door knob on the right side. When Debra Whitman is trying to get in the lab, the door knob on the outside of the door is on the right side as well, when it should be on the left side. The inside knob also disappears when the security guards break the door down.
Behold the Negative Zone - S1-E12
Factual error: When the heroes fly by the World Trade Center after Annihilus and Blastaar have begun battling each other, the 1 WTC building is missing its spire, and both buildings are incorrectly depicted as being conjoined by what appears to be a multi-level walkway. (00:18:13)
And the Sea Shall Give Up Its Dead - S1-E1
Other mistake: When Tony Stark is typing on the keyboard, some of the keys are depressing without him touching them.