I had villian squarely on a flush draw that missed...

Ultimate Bet Pot-Limit Omaha High, $.25 BB (9 handed) from (Format: Bet The Pot)

SB ($24.75)
BB ($15)
UTG ($32.30)
UTG+1 ($38.65)
MP1 ($24.88)
MP2 ($39.05)
Hero ($35.25)
CO ($53.50)
Button ($19.50)

Preflop: Hero is MP3 with , , , .
3 folds, MP2 calls $0.25, Hero calls $0.25, 1 fold, Button calls $0.25, SB completes, BB checks.

Flop: ($1.25) , , (5 players)
SB checks, BB checks, MP2 checks, Hero bets $1.25, Button calls $1.25, SB folds, BB calls $1.25, MP2 folds.

Turn: ($5) (3 players)
BB checks, Hero bets $5, Button calls $5, BB folds.

River: ($15) (2 players)
Hero ?????

first off, fold preflop. 4 suited cards are rarely playable and this isn't one of them.

If you put him squarely on a flush draw, check call. betting gets nothing unless he backed into a lower two pair or straight.

Yeah what Bri said. When I saw your hand my first thought was that you must have been in the big blind. That is not a very good hand preflop. And if you think he has a busted flush draw the only thing that makes sense is to check/call. I don't see why he can't have the straight draw as well though with AT9.