It's really not that hard to believe; it's just like with teachers: it's not that you failed the exam because you didn't study and spent your afternoons playing Xbox; it's because they didn't like you! No, but seriously, how do you justify writing up somebody who arrives 5 minutes early every day?
This can change depending on the culture, but pretty much universally, being late is arriving AFTER the time you're supposed to start. This employee not only arrives on time, but she's also arriving early, so how can the manager keep a straight face while telling her what he told her? That's why I say he might be coming up with a random excuse just to push her to quit. Those things happen.
She posted this in the subreddit /AmIOverreacting. Do you think that's the case?