Mathematics can raise concerns with a proposed physical theory by pointing out that it leads to discontinuities. According to popular belief, Galileo debunked Aristotle's thesis that heavier objects fall faster than light ones by an actual experiment, but in fact he proposed a continuity argument: if Aristotle was correct, connecting two equal falling masses by a string of negligible weight would double the mass of the object and thus cause it to fall much faster, which was absurd. (1/2)
@herid I believe there was some criticism by Greek and Arab scholars of at least some of Aristotle's theories (for instance, I know that his (rather strange) theory of vision was disputed by Alhazen, Avicenna, and others), but prior to Galileo I don't think there was a consensus on how to definitively refute a physical theory; in particular, Galileo is often credited with a major role in promoting the modern scientific method.