Hm........let me try and rephrase that. The Venasaur named Bruteroot, the Blastoise named Shellshocker, and Charizard each belonged to a trainer, the male one, female one, and Ash. Each trainer accepted Mewtwo's challenge to face a cloned version of their Pokemon, a Blastoise, Venasaur, and Charizard, all of them containing markings all over their body's. Since the clones defeated the 'original' Pokemon, the 'original' Pokemon were taken by Mewtwo to be cloned, but in the 'war' scene where the 'originals' faced the clones, there were only one Blastoise, Venasaur, and Charizard on the clone side, when there should have been two, the ones with markings that were there, and ones without markings, cloned from the male's, female's, and Ash's Bruteroot, Shellshocker, and Charizard.
I hope that was clearer.........or did I just make it more complicated 0.o