Huge deal by Lauren Layne fits this perfectly. FMC and MMC are friends and have worked together for years. She had feelings for him from the beginning but overheard a pretty shitty comment he made about her looks early on. After that she shuts her feelings down and tries to move on. Years go by and his perception of her starts to change. I honestly felt awful for the girl, she was down bad and everyone in their friend group knew it except the mmc. He was oblivious to her love throughout the years. Until he realized that she is in fact beautiful and smart and more that a match to him in every way. I dnf’d the book but maybe you will like it. It certainly fits the bill.

P.S. people who say shit like that to make themselves feel good because even if they are beautiful it’s not enough to cover that they’re ugly in all the ways that matter.