After Crysta saw the forest destroyed and the tree logging machine standing right there, why didn't the fairies just minimize the humans and explain to them what they're doing is wrong..or just minimize them? It made no sense.
This is Mike. He saves ghettos.
We're you looking for sense in an animated feature? How old are you?
shareTo answer your question, the fairies didn't shrink the humans because they thought humans died out long ago, but Crysta only shrunk Zak by accident and didn't know how to change him back yet. Also, even if the fairies wanted to reason with the humans by the time the film reached the climax, it wouldn't have worked, since Hexxus was already released and became too powerful to be stopped by only mere humans.
"Nobody expects the Spanish Inquisition!"