But that happens all the time in science, and we come up with different math that does explain it. Eg Jupiter's orbit couldn't be explained, the math didn't add up, so we came up with the idea that light had a speed and that Jupiter was far enough away that the speed impacted our calculations.

If you think about quantum mechanics, it's something that could sure look like a bug. Systems that you expect to be deterministic are stochastic if you look closely enough? If it were a program I was writing, I'd start wondering if there were rounding errors and/or concurrency issues. But we've come up with math to understand it.

Math is very general, I'm not sure there's a process that you couldn't describe with a complex enough mathematical system, and thereby conclude it had it's origins outside of our universe.