Not sure if this counts:
The Puerto Rican tody - a small, colorful bird - has the scientific name of todus mexicanus, even though it's endemic to Puerto Rico (where it's known simply as San Pedrito). Meanwhile, the todus portoricensis is actually a Cuban bird.
René Lesson, a French ornithologist, described the birds in 1838, based on information he received from his brother, who had collected some of the species and erroneously noted their provenance. AFAIK, there have been attempts to correct these entrenched errors, but there has been no success in doing so. To further confuse things, there are Puerto Ricans who will refer to the island bird as the todus portoricensis - perhaps as a way of correcting for the error, or just due to the confusion surrounding it.