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)
Six Forgotten Warriors Chapter 5: The Price of Heroism - S5-E6
Other mistake: When Spider-Man and Silver Sable are chasing the Red Skull and Kragov, they are able to deduce which direction they are going by identifying their footprints. However, Spidey and Silver Sable themselves don't leave footprints when walking over the same spot.
The Grim Reaper Wears a Teflon Coat - S1-E5
Other mistake: When the mob is throwing bottles at Stark Industries, the second bottle breaks in midair without actually hitting anything. (00:05:21)