Did I misplay this, or is it just unfortunate? or both?

25 NL. I raised to 1.00 UTG with 99, suits unimportant. Folded around to the BB, who re-raised to 1.75. This player was tight and somewhat passive so I immediately put him on AK or JJ+. I called and figured a set would be highly desirable.

The flop was Q9x rainbow. Gorgeous. The pot was around $4 and he led for $2. I don't frequently slowplay sets, but sometimes in position against a tighter player I will. So here I smooth-called.

The turn was an ace. Now he led... for $1? On a $8 pot? Suspicious as hell, right? I stopped to think about it. My planned line had been smooth call flop, raise on the turn, raise or value bet the river - the traditional "I have a set" line for 25 NL, in other words. Now I wasn't sure I wanted to raise. This bet seemed to scream one of two things: "I have a monster," or "I hate this board and want a cheap showdown." Considering he 1/2 potted the flop it seemed like the ace must have helped him, if he had a monster. If that was the case I could only make him for AA or *maybe* AQ. If it was a blocking bet, I put him on KK or JJ. Clearly I was way ahead of both of those and any raise here would get a fold, but he might bet again on the river or call a modest bet if I just called here. I was way behind AA so a cheap showdown would be great if I really thought he had that. If by some outside chance he had AQ though, I should raise to maximize value. The only thing I couldn't figure was if he would make that stupid re-min-raise pre-flop, OOP, with AQ.

This all was a lot to think about on Party's too-quick timers so I ended up just calling.

The river was a horrible ace for a final board of Q9xAA. He led for $5 (pot was $10), and I just called for the third time on a hand where I flopped middle set. And to be honest, I considered a fold (although not for too long). By that point I thought it was 75% likely that he had AQ or AA.

Horribly botched? I know there's a lot of non-standard stuff in here, but I thought his line was giving a lot of information away. What I'm not sure about is if I acted correctly given the information.

I've found that when I get minraised preflop like that by someone, especially from the blinds, its almost always AA or KK. I probably play it the same, or raise up to like $5 on the flop with the intention of pushing turn. I'm guessing you called and he showed quads on the river.

I'd raise the turn, and at least call river. If you fold poker is not the game for you.

No, I did indeed call. I was mainly wondering about the flop and turn. I don't think I can fold for 1/2 pot on the river, even though I was feeling sick as I called. I've been playing long enough that even though these were low stakes and this was not a huge pot with a lot of action, I still felt like I was probably behind and it was painful to call with a losing expectation.

I think you want to raise the turn for metagame reasons. No, seriously.
By flat calling his ridiculosly small bet, you are kind of letting him set the tempo. With a big hand (3rd set on a AQ9X board), you then forfeit your right to bluff raise a tiny turn or flop bet in the future.

Of course, it could (always) be an elaborate trap to get you to raise into AA or QQ.

In a vacuume, I think you played it fine because it's quite possible he has an even bigger hand, and not getting stacked after flopping a dominated set is quite a coup.