Both come from the same Latin root for the same (in contra), although the English one comes to us via the French influence: acointier.
Thus, we can see that the en-c-n-t-r maps to a-cqu-n-t somewhat closely: the final -r disappeared as the French word evolved into the English word, and the opening en- (in- in Latin) became the simpler a-.
Someone you meet, after all, is indeed your acquaintance.
There is, however, another English word that is closer to encontrar although perhaps less obvious until you hear it: encounter!
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