Many of those players are just bad returners. But, Fed is a very good 1st serve retuner. Maybe that's it. Maybe because he's so bad at returning 2nd serves, he just can't convert those BPs.
I don't know.
IMO he isn't that bad, yes more return oriented players like Rafa and Novak are going to be a bit better. Perhaps Federer is a bit nervous on break points in general, but ironically he does seemingly still win the most important points in each set/match. You can't have everything anyways
he is after all a very good break point saver himself.