Midoriya was ashamed of a lot of things about him - he hates how plain he was compared to the unique looks of his classmates. He hates how small and fragile looking he looks when he could handle breaking and shattering his bones time and time again. He hates how short he was; it seemed like a constant reminder that he still below everyone. He hates how he always subconsciously flinches away from touches thinking they were going to burn him. He hates how, when a hand gets placed on his shoulder; he feels the burning sensation that he should forget. He hates how he goes back to the thought of, 'what if I jumped off the roof, as bakugou said?'. He hates that he was quirkless and how everyone had treated him. He hates his freckles, for it was a constant reminder that his dad isn't here with him. He hates how high his voice is, and it makes him sound annoying. He hates his mumbling from how many times people have told him that it scares them, or it's annoying. He hates how useless he actual is because Aizawa is right; how could he be a hero when his power causes him to be a liability? He hates how he has a craving to touch people, to hug. Aizawa-sensei, to hold Uraraka, Todoroki, and Iida's hands, to be able to cuddle with his classmates and how fear is stopping him.
The thing he hates the most about himself is the scars he collected over the years. He hates the burns scars he has, the ones Bakugou left from when they were children to when they were teens. He hates how ugly they look on his skin, ruining his freckled back, shoulders, and arms. He hates the old self-inflicted lines running down his arms and thighs that he has to hide because who would want a hero who had cut himself? He hates the phantom pain that sometimes comes back, from when Bakugou blasted him in the middle of his back during the training exercise. He hates his mental scars too, always being worried that someone's going to burn or hit him the way his ex-best friend did. He hates that he fears his friends leaving him because what if Bakugou was right about him being good for nothing? A scar he'll never hate is the way his hand is crooked, with pale lines etched onto his knuckles.
He hates how he shouldn't be reacting this way because Todoroki was abused, and he wasn't - did Bakugou harm him? Does that count as abuse? He doesn't have the right to act like this because it's not happening anymore, and Todoroki is still stuck in the same house with his abusive dad; he doesn't have the right to complain when someone has it worse. Todoroki has the right to act the way he does; he has a good reason to be touch starved, to be angry at the world.
So, of course, he hated his body and learned to hide his body with concealer and make-up, so he doesn't have to show his scars or how ugly he is underneath his clothing.
For, He also hates himself.