Happens all the time in science. Science is about making our best current generalized explanation that fits the observed data. That's what gets us luminiferous ether, phlogiston, the plum pudding model of the atom, or the miasma theory of disease. Future generations will certainly look at us in horror for what our best current generalized explanations are, just as we look at previous generations.
That doesn't mean science is wrong or not worth pursuing. It just means we have to have healthy skepticism, which should be a virtue of science.
When I read history books, authors often mix these two. As a reader, I don't know whether a given statement is a fact (an artifact was found, several contemporary authors described an event in a uniform way), or just an interpretation that seemed plausible in a given situation