I haven't seen that movie, but time travel is some confusing stuff...
Surely if he dug up a protega fossil even though in the past it evolved, then he should have dug up a fossil of it's evolved form instead. If it's evolved in the past the event of it evolving in the future should never happen, because it already has. If that makes sense? It'd have to be a Protega in the past for him to dig up a Protega fossil in the future, but because it's evolved it rewrites time and he should have found it's evolved form's fossil at the beginning of last episode instead, haha.
Obviously I'm not taking it seriously or anything it's only an anime, I just tend to over think things sometimes
