Why do I still feel uneasy about ml

Because he's problematic. He never actually hurt the MC, though. He was creepy in the beginning, but I started to read it as being socially underdeveloped. It seems like he has a crush early on but didn't delve into it until near the end.

Yes, you're so on point. I find it very ackward how they show more action than actual communication. The ml just does stuff, but his thoughts are so one-sided..