It started very early on, back in 2006 DC and Federer felt he called an mto at an opportune time in a Djokovic/Wawrinka match and it escalated from there. Honestly, I think he saw the potential there and didn't like it and Federer was very territorial about his place in the game back then, and had a few choice words for Murray and Nadal in the press as well. But yea, it started off on the wrong foot and never recovered.
"Bad blood" is an interesting way to describe it. It definitely feels like there has been a real edge in their matches almost from the very start.
Roger processes losses better than any other player, but Novak hit a raw nerve with that Whodini like escape at 2010 USO, and we all saw Roger's pretty unfiltered response. You never normally see him respond like that in a presser.
Ever since then Roger has probably felt like he has left a lot of money on the table against Novak and is not particularly happy about it.