$40 river bet into $30 pot, has to be bluff, no?

[veryblind]

This is live $2/3 $100 buy-in game.

Hero has about $200. villain in SB has about $90.
Folds around to me on BN and I raise to $15 with 99.
SB calls, BB folds
flop: Ad Kh 7d
SB checks, BN checks
turn: As
SB checks, BN checks
river: 3d
SB bets $40

OK, so I'm pretty sure I made a mistake before the river so I deserved to lose this pot. I think check on flop is fine for controlling pot size though bet would be ok too, however I think betting flop turns my hand into a bluff (thoughts?). But I definitely should have bet on the turn.

Now, what can villain have that would make him bet $40 into a $30 pot. Made flush should be scared of full house, no? The overbet is neither a value bet or blocking bet. So what could it be other than a busted suited-connector?

The only other play I was scared of that he had a monster, (e.g. AK) and was trying to induce a call with a suspiciuos overbet. But this a rare play, even in live games where I think it happens more often.

If this hand requires reads, then I can provide some more info.

Also, if it makes a difference, this was villain's last hand before table change. And as I picked up my hand to muck, he whispers to me he hit the 3 on the river with pocket 33's. In retrospect, I should have asked him what suits he had to see if I can catch his eyes glimpsing back at at the board. But anyway, I don't to make this discusson about tells.

Thanks in advance