Based on her description of what the guy said it sounds like he was genuinely trying to just say something nice and she took it that way. As long as the email didn't follow up with a "so are you still single, let's get together" or whatever it's fine.

I think all the news of creepers out there and the Incel crowd makes it hard to see things through a positive lens, but there really are good folks out there. We all would benefit from assuming good intent when we see things like this.