I didn't even see it coming, what would you have done different? I figured he would be on TPTK

Not many people flat call a raise in a multiway pot with A9, then minraise a strong leading bet on the flop w/ tptk when their pair is only 9. A minraise on this board is usually strength...the board is very setty. I'd think he has 67/89/88/99/55 when he minraised, and since you're out of position with a vulnerable hand and no real draw, you can make a case for folding. However, if you call intending to check/probably fold the turn, that's better than this line...because you don't commit yourself on the turn. Notice how your $2 bet was more than half your remaining stack, so you basically told your opponent you were going to get it all-in. He's only calling/raising with a better hand there.

Bad thing about calling the minraise is that it gains you bad information by having to check the turn and see what he does. You're still only getting 3.6:1...you think you're winning/outdrawing more than 22% of the time? Seems unlikely given the way micro stakes players use minraises.

Fold on the flop minraise, and also don't overbet the pot. A $0.30 bet would have been fine, and if he raised to $0.60 you could still fold.