SB has an A weak kicker and is afraid you got a better piece of the flop because,
(1) You raised pre-flop x5bb, then post flop he bets half pot and you min-raise with only a gutshot/close ended straight showing.
(2) Turn hits, now he has to be afraid you had the Q. He can reasonably put you on any number of Q's. QQ,AQ,KQ,QJ..all hands you might raise heavy 3 handed. And even if you don't have the Q, you have him outkicked with your A that he thinks you might possibly have.
My guess, after checking it down he shows A4 sooted.