In addition to the appendix, my go to example of this is my friend's favourite organ: the Thymus [1]! If you've heard of "T-Cells" you indirectly know about it.

The interesting thing is that it is in a human when they are born, grows until puberty, then gets smaller and smaller until it can be quite small and difficult to detect in a grown adult.

I can imagine medical explorers cutting open dead 40 year olds in the year 1900, probably not finding any obvious organ there -- while perhaps cutting open dead children may have been a lot less common (and perhaps distasteful). If you did find something there, you would not assume an important organ present in a child and essential for their immune system would shrink and almost go away.

It would be more likely to be labelled nothing, an abnormal growth, or even a cause for death or illness (pressure on the heart/lungs!).