It's not a fallacy, and no one is saying "we see Y, therefore X is true." We are saying, if X is true we should expect to see Y. And we do that over and over and over again, for different predictions. And we evaluate predictions for alternative hypotheses as well. For evolution this has been going on for 150 years and everything we have learned about biology in that time has affirmed evolutionary theory. That gives us a strong indication that it is correct. Yes, it could also be a designer, but in the case of a designer you could say it was designed that way no matter what you see, which is why I say it is not falsifiable and therefore not science.