Messing it up

Villain 1 thinks that top pair is the nuts. Will bet out/call down with it, no matter what position, no matte what the board. Villain 2 is fairly tight.

PokerStars No-Limit Hold'em, $0.10 BB (5 handed) FTR converter on zerodivide.cx

Hero ($11.65)
UTG ($3.50)
MP =#A500AF(Villain 2)/ ($4.05)
Button =#A500AF(Villain 1)/ ($11.55)
SB ($6.90)

Preflop: Hero is BB with 9:club:, 9:spade:.
UTG calls $0.10, MP =#A500AF(Villain 2)/ calls $0.10, Button =#A500AF(Villain 1)/ calls $0.10, SB completes, Hero raises to $0.5, UTG calls $0.40, MP =#A500AF(Villain 2)/ calls $0.40, Button =#A500AF(Villain 1)/ calls $0.40, SB folds.

Flop: ($2.10) 9:heart:, 8:club:, 5:diamond: (4 players)
Hero bets $0.5, UTG calls $0.50, Villain 2 calls $0.50, Villain 1 raises to $1, Hero raises to $1.5, UTG folds, Villain 2 raises to $2, Villain 1 calls $1, Hero calls $0.50.

Turn: ($8.60) 6:heart: (3 players)
Hero checks, Villain 2 bets $1, Villain 1 calls $1, Hero calls $1.

River: ($11.60) J:club: (3 players)
Hero checks, Villain 2 bets $0.55 (All-In), Villain 1 raises to $1.8, Hero folds.

Final Pot: $13.95

Villain 1 showed J9o for two pair, Villain 2 76o for a flopped straight.

On the flop, I figured Villain 1 for A9 for TPTK and Villain 2 for maybe A6 for a straight draw. I think my turn check is pretty bad-if I think somone is drawing, why give them a free card? I didn't think the 6 made the straight for anybody, until I saw the action behind me. Maybe Villain 2 called preflop with A7? I think I'm beat at this point. However, is my call on the turn good? It's a 1 dollar call with 10.60 in the pot, and I count 9 outs to the boat (discounting the last 9 for quads, because I'm pretty sure Villain 2 holds it) for 5:1. When I missed, it was check/fold. The amazing thing is Villain 1 thought two pair was the best hand. I now realize my worst move was not calling Villain 1's raise after Villain 2 went all in. I stood to lose .55 cents, while I would have won 1.25, since my read of top pair was correct, and his jack on the river still didn't beat me.

I'd be interested in feedback here. Does my positional disadvantage make my preflop raise and flop bet bad? I didn't expect anyone would call with 76, but I still want to know if there was a way I could avoid this mess.

avoid this mess? no, not really. I noticed this is a no-limit table, and I think you should've bet out more on the flop. like you said, villan one will call down with TPTK, and you want to make him pay, right? and you also say you think villan 2 might be on a draw, so you don't want to give him good odds to draw, right? (which you were doing on the flop) I think a $2 post-flop bet is the best play here.

on the turn, it's 4 to a straight, so the check isn't a terrible play. assuming I got called on the flop, I might throw out another bet around $2. even if someone has a straight, you still have 10 outs to make a full house.

It sucks that someone flopped a straight on you when you made top set, but hey, that's poker.

Your flop play was pretty bad, you hit top set on a pretty scary board. At this stage I would not give anybody credit for 67 (while call a PRF with it?) but pocket 6 or 7 is a possibility.
Villian's 2 behaviour on the flop is wierd, he called your initial bet and then reraised villian1, this screams a made hand - I would put him on a set here and pushed.

On another note, your assessment on the river mistake is correct , however your conculsion is wrong - you should have raised him by the max amount you believe he will call