Ghost Rider VS Lobo (Marvel VS DC) - S6-E10
Audio problem: When Ghost Rider drives up and points at Lobo, he starts speaking. His mouth is moving, but when it cuts to a different angle just before Lobo runs him over, his mouth is now not moving while he's still speaking.
Other mistake: When Shao Kahn rips M. Bison in half, M. Bison's hand is ripped apart too... and then stays attached to his body somehow.
Nightwing VS Daredevil (DC VS Marvel) - S5-E12
Daredevil: I wish I could see the look on your face.
Nightwing: Me too. (00:17:15)
Trivia: This was the first episode of the show with actual voice acting.