He's not a very tactful guy.
I wouldn't feel bad about it. Most people look a little better and more rested with some make-up on.
I remember back when I was in school. There was one girl who wouldn't wear makeup if she was planning to skip school the next day.
The teacher would ask her if she's not feeling well and she'd play it up.
I'd worry if he didn't recognize you at all but looking like you just woke up is perfectly fine. I think he was just trying to figure out what you looked a little different.