when astronomers measured an error in Mercury's precession of the perihelion that couldn't be explained using Newtonian physics. The error was only 43 arc-seconds per century (an arc-second is 1/3600th of a degree) but that was enough to cause problems. That error gave support to the Theory of Relativity, which was better able to explain what was going on.

It's possible these new measurements will lead to new and better theories. That's the beauty of science - no divine wisdom or revealed knowledge, just a process that continually seeks to better explain how things work. In the case of Mercury, it took decades from the time the error was first measured before the Theory of Relativity could explain it. No one said these things happen overnight.