Yes, and many of these wins came in 2008, when Fed also lost to guys like Blake, Karlovic, Roddick and Fish, players he usually owns. Federer, as much as I hate to admit it, is no longer in his prime and is near the end of his career. In 2008, he played some matches so bad, I thought maybe if I'd play against him I could win. OK, not really, but still it was a horrid play for most of the year. The fact that he still gave a lot of trouble to the top guys despite playing so bad is amazing.
But leave the H2H for a while.
Take prime Murray, prime Nadal and prime Fed. Make some matches between the three on hard courts. I'm confident Federer will win most of the matches, with Murray being second, and Nadal third. On grass, it'll Fed first, Nadal second, and Murray third. On clay it'll be Nadal of course, and then Fed, with Murray not doing much to either.
The H2Hs are worthless. Federer has a losing streak against Nadal, but he has a winning streak against Nalbandian and Blake, and Nadal has a losing streak on HC against Blake and Nalbandian. What does it say about the best of the bunch? Nothing. All it says is that a player is a bad matchup for another player who is a bad matchup for the first player.
The best player is the player who can be very consistent (despite some losing records) and win slams. And that's Roger.