Both "but" and "and" are conjunctions, meaning they are used to join together two independent ideas. As far as I know, every language has some version of these. As with most languages, "but" never means the same thing as "and" as it implies contrast rather than sameness. For example.
He was small and mighty. (he is both of these traits)
He was small but mighty. (in spite of the first trait, he is the second trait)
As in other languages, how much of a contrast depends on the context. It can be so small that either could be used:
I was late to the party, but it was a good thing, because my friends were also late.
I was late to the party, and it was a good thing, because my friends were also late.
Nevertheless, "but" enhances the contrast while "and" diminishes it. In your example sentence, it seems important to create a strong contrast in order for the sentence to make sense:
The animal was originally incorrectly classified, but only because experts at that time agreed it was the best possible fit. Later, it was re-classified according to an updated understanding of its taxonomy.
When you state the assertion in this way, it's clear "and" doesn't fit.