Bucky wasn't exactly doubting that Scott is a good guy. If he's working with Steve, then he's not going to be a bad guy, and he hardly has any room to judge. Not with the amount of blood on his hands. It doesn't matter that HYDRA were the ones to pull the trigger, he was still the weapon.

"You know that he's here?"

Steve, he means, not Sam. But he doesn't bother to clarify.

"You don't tell him that you've seen me."