His hand plays ridiculously better than yours after the flop. On low two pair boards you can hesitate about putting in lots of money but he needs as little as a pair and a gutshot with a few overcards before he can put in the rest just because how often so much more of his hand is live.
Flop play, he probably just figured one of you has the nut flush and would be unable to fold it. It may be exploitable but he avoids bad things happening. If you did have bottom set, it checked around and the turn was a queen, stacking off would still be pretty awful.
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