Maybe Johnathan remembers Willow as the interrogator in "Earshot":
WILLOW Fantasies are fun, aren't they Jonathan?
JONATHAN Uh... I guess.
WILLOW We all have fantasies that we're powerful, more respected. Where people pay attention to us.
JONATHAN Uh... maybe.
WILLOW But sometimes the fantasy isn't enough, is it Jonathan? Sometimes we have to make it so people don't ignore us. Make them pay attention. You know what I'm talking about, don't you?
JONATHAN Em, you... Want me to pay attention?
Willow looks a little flustered.
and later on:
WILLOW Jonathan! Oh, I had him in my grasp. Slippery weasel.
Quotes are from:
03x18 - Earshot - Buffy the Vampire Slayer Transcripts - Forever Dreaming
Before that, in "Go Fish", she had interrogated Johnathan about the disappearance of some of the swim team:
Cut to Willow's classroom. Jonathon is sitting in a chair at the front of the room. Willow aims a reading lamp at him. The camera pans from it up to her face, determined to get what she wants out of him.
Willow: So, Jonathon. (crosses her arms) You tried out for the swim team twice and never made it?
Jonathon: (fidgets) I'm asthmatic. I couldn't keep up.
Willow: You resented it, didn't you?
Jonathon: Maybe.
Willow: (approaches him) You hated being pushed around by Dodd and the others.
Jonathon: So?
Willow: (walks around to his other side) So, you wanted revenge. Didn't you? (leans in suddenly) (sternly) Didn't you?!
Jonathon: (nervously) Yeah! Okay? I did!
Willow: (smiles and straightens back up) So... You delved into the black arts and conjured up a hellbeast from the ocean's depths to wreak your vengeance.
Jonathon: Huh?
Willow: Didn't you?
Jonathon: (confused) What? No! I snuck in yesterday and... peed in the pool.
Willow: (disappointed) Oh. (disgusted) Eww!
He looks down in shame.
Read more at:
02x20 - Go Fish - Buffy the Vampire Slayer Transcripts - Forever Dreaming
On both of these occasions, Willow had completely dominated Johnathan, who he never wanted to converse with again. He was afraid of her. I am not sure he was all that cognizant of Willow being a witch or having powers anywhere near his own. I am not sure Willow realized this was a spell that Johnathan had cast - she was caught up in the same Johnathan mania as everyone else and Johnathan had no reason to suspect she would ever challenge him on it.