I've had two encounters with this this year. The first was learning that appendixes* almost certainly do have a function: as a reservoir of healthy gut bacteria, for repopulation after digestive ailments. Appendixes have been thought so useless that my mother (to give an example) was given an involuntary one, while the surgeon was operating in that general area anyways.
More recently, reading about the anatomy of lactation, I learned that until 2005, lactiferous ducts were thought to dilate into the "lactiferous sinus", which stored breastmilk; but further study showed that the lactiferous sinus does not exist. (Encountered on Wikipedia, source is here.)
If a previously-assumed part of the body can be shown to not exist in 2005 and the use of another to only be hypothesized in 2012, then people of the seventeenth century - and earlier ones - certainly have nothing to be ashamed of, living when they did, in guessing at other plausible explanations for the function of the heart and the movement of blood.
* I keep wanting to type appendices, but then you'll think I'm talking about books.