I wouldn't necessarily this is a problem with a 'specific hand' ie. '99' To me it just seems like you played it poorly.
Preflop. Call is okay (could also consider a 3-Bet here depending upon history & Villain)
Flop the Check-raise is fine.
Turn - Why are we over betting POT when some potential draws just got there? This type of bet in this spot is going to make you 'win the least' and 'lose the most'.
River - you continue by putting villain all-in (even after they've called the check-raise on flop, and the huge overbet on turn). What worse hand combos do you figure got here in this spot that are still going to call this bet? What better
hands are going to fold?
You've basically turned a flopped set into a
bluff & value-owned yourself.