With HU, you and your opponent are playing way more hands than you normally would in a FR or 6Max game(at least you should be), so this is going to happen more often. In a FR or 6Max game, middle pair on the board isn't much to think about when you know you have a couple others in the pot, but HU, you could very well have the best hand, so people will play the hand like that unless something big happens. Also, what are you determining as a suckout? Like you two get allin on the flop while your set or two pair vs his flush draw? Well in those cases you are winning right now, but it isn't like you're up against a 1 outer, 75% with the set and 65% with two pair. Sure, you're happy to get it in with that, but you can't be surprised when that 25-35% comes down, whether it's two hands in a row or two hands in an hour.
I'm guessing that there are probably some betting problems on your end as well, but without seeing any specific HH's, that's just a guess.