Perhaps he just had his own batch without the kill order receptor? If that was even allowed.. I mean, maybe Yoda was allowed his own personal honor guard of sorts.
Nah, they weren't Yoda's personal guard or anything, they just follow Yoda in a couple episodes, and do a bunch of other stuff with other generals in most of the rest. Remember in the movie, Yoda *was* attacked by clones when the order was given.
EDIT: Hm, I may be getting the clones wrong, Wookiepedia says there were 3 or 4 squads that explicitly disobeyed the order (just faked it and were all "must kill Jediiiii" but didn't actually do it, even helping some escape). I think one was the squad from that Republic Commando game, another was from some novel, and another was from the first batch of clones which didn't have all the free will properly pound out of them. The Order isn't so much a Mental compulsion as it is just a legal order that they're trained to obey, being the good and loyal soldiers that they've been bred to be. So while it's possible to disobey, apparently only like 1% would even consider to do so.
(I would think also that something like 98% of the Clones weren't even near any Jedi at the time, there being only a few thousand Jedis and millions of troopers), so it was all like "hey clone dudes, if you see any Jedi, make sure you kill em, ok?" and they were all like "ok, sure, whatever dude" and then spent the rest of their lives never meeting a Jedi.