Analysis of Harry's conversation with Snape in ch. 27.

"If he were a friend," Harry said, "all the more reason to forgive him."

Possible Snape thoughts: "He implies that I wasn't even a friend of She. How dare he!?" ... consideration of different ways of mutilation ... then "Oh! He can't possibly be like his mother. She had a very high standards for Her friends. Maybe his stepparents taught him this indiscrimination of friends."

"She was shallow"

"SHE was shallow!? ... But She married that brat Potter. Was Her standards high after all? Maybe not. And I gave all the power I could have for her..."

So I think Snape became misogynous. Thus Alissa's affection became irritating for him. I don't know what implications it will have for storyline however.

Edit: Analysis is done by Type 1 processing with Type 2 postselection, so no justification is given. :)

Edit: This hypothesis seems to be insufficient for explanation of emphasis on "wrong" in Aftermath 2, maybe there's something more.

Edit:

1. "Wrong" can mean, that she was aware, that Snape isn't kind of person young woman is supposed to crush on. I'm not sure that this is true for Slytherin. Anyway Snape isn't handsome guy, it's not deserve emphasis to hint that.

2. "Wrong" can mean, that she feels it's bad for her to show affection now. Fits my hypothesis, but not wording "There was probably something really wrong with her...", which imply that she knew it all the way.

Some part of puzzle seems to be missing.