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
Nightwing: What are you?
Daredevil: Better. (00:16:10)
Trivia: When Scorpion catches Ryu's fist, we get the first 2 hand-drawn shots in the history of the show. (00:12:00)