I met an old classmate today, and after hanging out for a while, I said a good joke. Her response was a small laugh accompanied by saying, "You are less annoying than I thought you'd be by now." I genuinely didn't know how to feel about that, and I just mentally noted it down as the weirdest compliment I've received so far in my life. What's yours?
You are distinguishing positive/negative based on your imagination. I'm not that friend of yours so I'm not sure about the intention behind it but you can frankly ask about it with the other person.
In the case that happened to me, there is nothing strange, perhaps I prefer to hear appreciation rather than unrealistic things. Like a teacher once said "you tried but it wasn't enough"

I was really happy when I realized how much it means to have satisfaction and gratitude from these messages through language communication. Anyway, sometimes it can be doubtful to distinguish things that we imagine in different directions, but perhaps we should also go back and live fully with the things going on around us without clinging to something that someone offers.
Well to be honest, saying "you tried but it wasn't enough" is pretty far from weird. It's intact a way of motivating you to do better so credit to your teacher there. My post here however, is referring to those kinda compliments that you didn't know whether to interpret as either positive or negative. The ones that just fall in-between.