The Pokemon that you can see in that shot isn't a Nidoking, it's a Nidoqueen (Nidoqueen is blue whereas Nidoking is a distinct purple). The trainer who owns her is the same one who has the Gyarados; none of them have a Nidoking.
I've watched that scene again, and would like to make a correction. ^_^; In just one shot, the Nidoqueen is coloured purple, like a Nidoking. But compare it with the Nidoking that Gary uses to battle Mewtwo earlier on in the movie. The spikes running down a Nidoqueen's back are all separate (unlike on a Nidoking where they're joined together in a ridge) and the ears aren't tufted, they're pointed (Nidoking has small tufts on the ends of its ears). In other words, the Pokemon there is still a Nidoqueen, but she was accidentally given Nidoking's colour for one shot.
Ummmm if i can point somthing out? a nedoking and nedoking dont always have the same colors they could be shiny colord pokemon? is all im saying. if a person is good enough to battle mewtwo i think they have a shiny pokemon
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