Origin of Iron Man: Part 1 - S1-E11
Character mistake: When young Tony Stark is telling his father that their helicopter's anti-flak chip didn't kick in, he acknowledges that it was his fault by saying he blew it. When his father corrects him and says "No Tony, we blew it. Stark and Son," Tony defensively says "The anti-flak chip failed, it's not my fault," completely contradicting what he said seconds earlier. (00:14:00)
Behold, a Distant Star - S2-E10
Character mistake: When Sue is brought out of surgery, her father can be seen wearing a watch. Surgeons don't wear watches or any other kind of jewelry when performing surgery, as they can't be sterilized and can also get in the way of gloves. (00:05:00)
Spider Wars, Chapter 2: Farewell Spider-Man - S5-E13
Character mistake: When Stan Lee is asking Spider-Man what he plans to do after saving all of reality, he responds by saying to find the real Mary Jane. Moments later in the final scene, Madame Web tells Spider-Man that she is taking him to find the real Mary Jane, which elicits an incredulous response from Spider-Man, as if he didn't know that was already the plan.