Distant Voices is the episode that gave Bashir complexity, and the genetic twist paved over it.
That's one of several episodes that prove that making Julian an enhanced human was DS9's biggest continuity problem. After all, the Lethean who telepathically attacks him certainly should have known his secret and used it against him in that episode.
Another episode would be "The Quickening" when Bashir said he was capable of sewing up his teddy bear at age 5. Since in "DBIP", he mentions he was enhanced around his 7th birthday, it's very unlikely he'd have been able to patch up the bear if he were deficient and uncoordinated 2 years before that.
You could even add "Q-Less" to the list if you play your cards straight. Someone as omnipotent as Q would certainly know the secret and could have slipped in a little hint in the scene he induces Julian to sleep over the remaining part of that episode. When the Doc departs from that scene, Q could have said something like "You're still inferior to the likes of me no matter what they did to you." Being it was in the first season, that would leave viewers wondering what he was talking about with the answer finally coming 4 seasons later.