It wasn't a misunderstanding caused by his poor wording; It was caused by poor (and possibly malicious) misquoting.
He has nothing to apologise for in this respect, but he does say:
> I'm sorry for that hurt. I wish I could have prevented the misunderstanding.
This could be seen as an apology, "I'm sorry" often is; but in context you can see it is not. It is literally "I'm sorry I could not prevent this hurt" without any sense that He is responsible.
Ironically, this sentiment only brought on more criticism: The claim that this was a "false apology", i.e. something masquerading as an apology despite not being one - but that was Stallmans intention, it is thwarted by all the other sentences in the same paragraph that make it clear he is being misquoted.