Were there ever empirical facts that were later disproven? Or is that a contradiction?
A fact is not something you prove or disprove, it is a statement of something you have seen or observed. For example that the orbit of mars is an ellipse not circle is a fact, based on observations by Tycho and others after him. Now the accuracy to which we know the details of that has of course gotten better.
There have been some things that were taken as facts over the years that came from measurements that we conducted incorrectly, or in some cases out right fraud. (It happens)
But in general things taken as a fact in science have been tested and retested in many different ways over the years. For example relativity has been tested in thousands of experiments over the last 100 or so years and has been found to be correct in every case.