I think the argument is mostly that there are universal truths than math and physics describe not that our current level of math and physics are universal truths. So finding an example that we do not understand fully doesn't mean that there aren't truths in other aspects of math and physics. As for things like complex numbers there is an underlying debate that has been around in philosophy of science and math that distinguishes between discovery and invention. Our representation may have been invented but we discovered some thing that works historically and has predictive power.