When Ash rescues Pikachu from the clone machine, and Squirtle and Bulbasaur get released from their original poke-balls, Ash's English voice laughs, but his lips seem to be saying something, not "laughing"
In the mini movie, Pikachu's Vacation, when Pikachu is strolling along and the Pokemon run over Pikachu, Psyduck also runs on top of Pikachu, and runs off with the crowd. Then when the camera pans to the right, Psyduck is with Bulbasaur, Squirtle and Togepi.
After the real Charizard, Venusaur and Blastoise have battle cloned versions of other Charizard, Venusaur and Blastoise. Mewtwo "claims his prize" by capturing most of the pokemon (not his own, and some of the trainer pokemon are missed such as Misty's Togepi) so he can clone them which would result in 2 clones of Charizard, Venusaur and Blastoise (original and new) yet we only ever see the original clones.