The story is told from Seodan's pov, he's an inexperienced virgin so he views everything in an extreme way, and everything that happens to him is more scary and violent than it really is and is different from ml's pov.
They will discuss it more in later chapters, and even though ml thinks he didn't do anything that needed a safe word he still apologizes for not considering Seodan's perspective in their play later on
True, he's not a good dom purely for ignoring his sub's wishes when he used the safe word when they had penetrative sex for the first time. He said it was because he didn't consider that 'play' and they were just having vanilla sex, but still he's a shitty person for doing that.
But what i love about this novel is that it doesn't gloss over ml's actions and he admits to being unethical and having issues, he heals along with the mc the more they spend time together and he finally understands himself and purpose.
When did he "beat" him?