The Origin of the Fantastic Four: Part 2 - S1-E2
Deliberate mistake: When the Thing is doused with the chemical that reverts him back to human form, he somehow also is suddenly wearing a T-shirt, jeans with a belt, and shoes, which is illogical since the Thing wears a speedo with no shirt and is barefoot. (00:05:35)
Superskrull - S1-E7
Deliberate mistake: When the Army soldiers are all walking towards Super Skrull, they all have the same face. (00:14:57)
The Mask of Doom: Part 1 - S1-E8
Deliberate mistake: After Thing destroys the mirrors, the shot of him, Reed and Johnny traveling through the corridor is recycled footage of the corridor they traveled through to get to the hall of mirrors in the first place. (00:19:08 - 00:19:49)
Answer: Gleaned from the Internet: Much of the negative reaction was due to the poor, simplistic, and outdated quality of the animation where the characters moved stiffly and clumsily through scenes. There were also some obvious animation compositing gaffs. The animation colors were also criticized as being overly bright and cheery and out of character to the established story's darker tone. The broad humor of the first season was replaced by a more mature narrative between the characters.
raywest ★