It's normal, it happens but even if there's an anomaly, it's in Greek, not in Latin.
The story behind this is that actually quite often cognates (word of common origin) designate related yet different concepts in related languages, and zoology terminology is no exception.
The Latin word is reconstructed from from Proto-Indo-European, here's an excerpt from the article:
From Proto-Indo-European *kápros (“buck, he-goat”); see also Old Norse
hafr (“he-goat”), Old English hæfr, Welsh gafr, Old Irish gabor.
Which is actually not precise. What is more correct to say that we can assume with high probability, we can claim that most likely this word originally stood for goats.
Most likely (the ancestry we have in Indo-European languages) it indeed meant a goat or something close to goat. But first, there's still a probability it's not the case. Second, even if it is a case, that proofs nothing.
What's common between a boar and a goat? Those are big hoofed animals.
Say, in German we have Tier, an animal, which is cognate to English deer. One can ask why on Earth this happened, but the answer is pretty obvious - it's just that languages evolved in different directions, so that the set of possible meanings for specific root X in language A and set of possible meanings for the same root in language B do not intersect anymore.
As a sidenote, Latin word for boar was aper.