First off, a true scientist would never admit that we know everything about something. And of course science can make mistakes - especially in biological related fields - it's full of dynamic systems and it is difficult to control for all variables.

About the trees/deforestation - it's all about moderation/equilibrium. In most cases too much or too little of anything is a bad idea. And until we build a time machine of some sort, we'll never fully know the long term effects of certain things (in your case, genetic engineering; not what I would use for an example - but I won't get into my GE/hybridization rant) until it's too late.