Unforeseen consequences are a thing, and nature can evolve in difficult to predict ways. For instance one of the big early arguments for GMO crops is that it'd enable us to reduce our overall usage of herbicides. The main modification was glyphosate resistance, and since glyphosate was otherwise highly toxic to all plants, it was thought that just a bit of it would be enough to take care of what used to require much more herbicide.
And it lived up to this promise at first. But nature responded by naturally evolving glyphosate resistant weeds, and farmers responded by just spraying more of it, and more regularly, and we're now using more herbicide/acre than ever before. In 1991 (just prior to GMO crops starting to really kick off), we were using a rate of 1.18 units of herbicide per acre. By 2000 that had declined to 1.06. "Now" (2014) we're up to 2.02 and rapidly increasing. [2]
So many things (related to interacting with nature in various forms) seem to be being done under the assumption of a stationary target, when nature is anything but.