[Deathknight]

Yeah, there were a couple of episodes that had missing bad guys like that... off the top of my head, Back to the Egg had Shredder and Krang but no Bebop and Rocksteady, the Maltese Hamster and Corporate Raiders from Dimension X (like you people mentioned) have shredder, bebop and rocksteady but no Krang. Turtles of the Jungle also had Shredder and Krang but no Bebop and Rocksteady.. I'm not going to bother my brain anymore tonight to think of anymore examples but here are the official vhs I own:
Heroes in a Half Shell(Turtles Tracks and Enter: The Shredder_
Hot Rodding Teenagers From Dimension X( with A thing about rats)
The Shredder is Splintered (Return of the Shredder)
Case of the Killer Pizzas (Enter: the Fly)
Cowabunga Shredhead (New York's Shiniest)
Super Rocksteady and Mighty Bebop (Mutagen Monster)
Attack of Big Macc (Old Switcheroo)
Pizza by the Shred (Return of the Fly)
Beyond the Donatello Nebula (Big Bug Blunder)
Unidentifed Flying Leonardo (Foot Soldiers are Revolting)
Planet of the Turtleoids
Return of the Turtleoid(Zach and the Alien Invaders)
Leonardo Lightens up (Leonardo Vs. Tempestra)
Donatello's Degree (Donatello Makes time)
Raphael meets his match (Raphael knocks em dead)
MIchelangelo Meets Bugman (Badly damaged) (What's Michelangelo Good for)
Also waiting for from ebay:
Big Blow out (Peking Turtles)
Four Turtles and a baby (Shredder's Mom)
Big Zipp Attack (Farewall, Lotus Blossum)