I think the issue is that Stark seems oddly upset that Cap would choose his best friend over him. It's not like Stark is in life threatening danger so what's Cap's motivation for picking Stark?
I dunno, it's impossible to say without seeing the movie. When he says that line though, it's after he gets that shiner over his eye. Chances are Steve is the one that punched him.
In any case, the situation dissolves into violence which is likely more than Tony expected. Tony is just pointing out how their friendship didn't seem to factor at all to Steve.