The Defection of Hawkeye - S1-E8
Deliberate mistake: When Mandarin is watching and wondering why Julia is tailing Clint, the road surface and cliff walls around Julia's car are recycled repeatedly. (00:10:55)
Did You See the Sun Rise? - S3-E1
Deliberate mistake: When TC is flying the stolen Loach toward the Japanese delegation, there are multiple exterior flipped shots showing the stolen helicopter backwards. There are also flipped closeups of TC while flying, note position of his helmet mic, etc. (00:34:35)
Deliberate mistake: To fix the error of the Enterprise firing phasers from the torpedo bay, the Blu-ray version uses footage from "The Best of Both Worlds" to show phasers firing from the dorsal emitter. In doing so, they created a new goof; the planet El Adrel is not visible in the background during these shots.
Suggested correction: I rewatched the original version on the old DVDs. El Adrel wasn't visible in the original either, so this is not a new error.
Going Rogue - S1-E4
Deliberate mistake: When Capt. Cold is about to shoot Joe in the train station, Eddy "shoots" a pillar next to him to make him run. Eddy then comes from behind the pillar that got shot with no cuts. He would have had to been on the complete opposite side to shoot the pillar where it was hit. (00:32:50)
Suggested correction: I watched the scene several times and nothing indicates the pillar was shot from the left side. It looks like the pillar was shot from behind (which is why there's no hole on the side or front), exactly where Eddie would have been standing.
The Secret of the Unicorn: Part 1 - S1-E3
Deliberate mistake: After Francis Haddock kills Red Rackham, he lights a fuse to the explosives. The fuse that was lit is only a foot long, yet he is somehow able to climb out the ship without anyone noticing, get into a boat and swim all the way to land before it explodes. At a foot long it would have exploded in 10 - 15 seconds, all of that would taken at least 10 minutes. (00:18:45)
Formidable Enemy!? Mother Coordinator Enters! - S7-E37
Deliberate mistake: This Pokémon Trainer's Choice segment incorrectly claims that Arbok evolves into Seviper, which isn't true. (00:11:38)
Genesis (2) - September 13, 1956 - S1-E2
Deliberate mistake: When Sam ejects and lands on the ground, the closeup is a flipped shot, note the "US Air Force" is backwards on Sam's helmet. (00:19:10)
Deliberate mistake: Throughout the episode, all the police station clocks are still and show the same time (3:33) in different scenes. (00:18:55)