It sounds like Ito probably missed that news, which I think is what folks have a problem with — he should have done his research before accepting the money.
I think there is also a separate debate here about whether Ito should accept or reject money from a donor who he knows is a sex offender.
Edit: seems like people are assuming he did know about that past, which is unclear to me.
Its possible Ito didn't know initially, but its pretty implausible someone didn't tell him about it once he started introducing Epstein around the lab.
I think that's the problem with the apology, he doesn't actually say what he's apologizing for. It's pretty clear that he's apologizing for taking money for someone he new was a sex-offender, but he doesn't actually say it, nevermind apologize for it.