I just realized that the person who snuck doubt about Sherlock and his capacity for relationships into the back of John’s mind was Donovan from ASiP. She, just like in TRF, was solely responsible for planting the suspicion. Sherlock left John without explanation in ASiP to track down the suitcase and Sally was there to make sure John stayed cautious of this person forever.
If only Molly Hooper had been the one to talk to John that night – or Mrs Hudson – they could’ve instead said, “He’s not coming back. He does that sometimes – gets lost in his head, that’s all. He doesn’t have many friends, but he must really enjoy your company. He wouldn’t have invited you there if he didn’t. He’s a good man, has a good heart. He just doesn’t know how to communicate his feelings very well”.