Isn’t there a rule that what comes from a non-kosher animal is non-kosher? Since a bee is non-kosher, how can honey be kosher?

The Gemara (Bechorot 7b explaining Vayikra 11:21) offers two explanations: One is that the bee processes the nectar that it stores and converts to honey, but the honey does not actually come from the bee itself. The other is that there is an inference that consumption of bee honey is permitted.