With the 3 undercards on the board, I think that this is a pretty easy river flat. He could have been calling with a straight draw and hit. There are only bluffs and a couple of trips hands you beat here, because 93/94/95 are gone so you beat 92/96/97/98 and lose to all other 9s.

The first thing I notice is that you min bet led the flop.A lead can be fine, however, if you're going to make it lead for a larger bet.  You're deep and you want value, so a pot sized bet actually makes sense here.And honestly, an overbet isn't even terrible here, I'd actually prefer it to a min bet.  All those guys you see attacking limped pots with overbets?  They can actually be very good plays, completely dependent on the frequency of their bets, hand selection and opponent's characteristics.  But that's a spot you can certainly exploit opponents.  If he can't fold a flush draw (and he's a horrible loser so he is likely a pretty loose or incredibly weak opponent) to a 60 bet into the 40 chip pot, why not bet 60?Now, the other option is a check raise.  Check raising can build a pot this deep, which is incredibly valuable when you have a strong hand in a limped pot this deep.  You allow him to bluff with his entire range and you commit his calling range to a much larger pot (extracting more value on this flop than if you had led).  Don't be afraid of betting or raising too large in these spots, you'd much rather have him fold to a big turn bet in a decent pot than to price him in and end up misplaying latter streets (and losing value on earlier streets). The disadvantage of the flop check raise is that he can check back.  Generally speaking, you'll want to check raise a more aggressive flop bettor and lead vs a more passive one.  No reads?  Lead larger or go for the check raise.  If you miss the check raise don't be afraid of making a large turn bet for value, you already missed a street of action and you want max value from any of your opponent's range that might call a big bet on the turn (almost always better than making a small bet on the turn, you just end up in so many crappy spots vs unknowns where value vs fold vs call vs raise is literally impossible to figure out, plus you don't really charge the draws and random hands enough by making small turn bets in limped pots deep).As far as how the hand played out, I agree with monkey.  With the weak flop bet, a lot of hands are in his range going into the turn.  Once he calls the turn bet, his range is still somewhat wide, with all the straight and flush draws out there.  Some draws were made on the river, and the cards are low on the board, also a single pair is less likely to call a reraise (and raise in the first place) on a paired board where flush and straight draws did hit.  So a flat call is absolutely essential on this river.  However, I think examining your flop play is the most worthwhile part of this hand.  It's something that can really help you stay out of trouble spots, keep people from being priced in (or close to being priced in and thus giving you less value with drawing hands) with a wide range of hands and thereby preventing you from making many more mistakes on latter streets.