Bonobo
Until the late 1920's the bonobo was not considered a separate species from the chimpanzee. When the species were finally separated based on skeletal differences, the bonobo was given the name "pygmy chimpanzee", which feels inaccurate not only in that they are not just a smaller version of the chimp, but a vastly different animal behaviorally, and also in that the size difference between the two species is overlapping, and not significant enough to warrant the term "pygmy".
The word "bonobo" is probably a misspelling of the village Bolobo on the Conga river, and is also a curious choice for a name since the significance of the village is debatable.