Continuity mistake: When Beavis is getting the idea to use the plate as a discus, the amount of cookies on the plate varies depending on the shot.
Enemy Within, Enemy Without - S1-E6
Revealing mistake: When Iron Man tells MODOK that his wife is waiting to see him, MODOK's nose and a section of his headband are briefly missing from his face. (00:19:49)
Heart of Archness: Part III - S3-E3
Continuity mistake: On the way to the helicopter, Archer stops the group to ask about the lacrosse game. Archer has the pirate held at gun point and the two are standing mere inches from each other, but when Archer says to Lana she is his only friend, the pirate is nowhere in sight.
Midori no chikyû wa makasetoke - S1-E2
Other mistake: When Yurika restarts the Nadesico, one of the screens pop up with a huge congratulatory "SAFATY ROCK OFF." (00:18:05)