So probably using the same implanting memories stuff they did on Natasha, Hydra (as part of being evil, breaking Bucky, or just preparing Bucky to kill Steve) convinces Bucky that Steve participated in his rapes (and other general abuse) and/or abused him before he fell. The memories are buried, of course - maybe happened when he was initially being programmed, maybe it was some techie goons messing around with the mind wipes until Pierce found out and shut the whole thing down, etc - but they slip in among the other memories as Bucky slowly recovers.

Initially it's not much. The flash of a face. His voice. Could be mistaken for pre-War consensual sex, or Bucky getting confused and inserting Steve into his nightmares. Except then Bucky starts getting back more and more, and it's looking a lot like the same shit Hydra put him through. In fact, he strongly begins to suspect that Steve was abusive pre-fall/ is actually part of Hydra/ has abused him since his return and mind-wiped him.

(None of it is true, of course)

Would like if Bucky (at least eventually) realizes the memories are false (or at least desperately tells himself they must be) but still has flashbacks and panic attacks about Steve hurting him