Bones creator Hart Hanson explained, "Between the shock of being put after Idol, and then [planning] the spinoff, and rearranging our schedule, it threw a grenade into our episode order and it's been a real chore getting it back together again."
Apparently, playing episode musical chairs happens all the time in the TV world. One reason is simply that the showrunners realize that it benefits the storyline to make some rearrangements. But other times, like in the case of Bones, the show may get moved to a different time slot and need to consider a potential new audience.
Hanson acknowledged that the new show order is "very different" and that producers had to "bend Heaven and Earth to make everything work."
He added, "The thing that's been difficult is making sure that everything stands [and] that the audience won't notice that the order changed, because we can't interfere with those arcs." Having "The Body in the Bag" follow "The Doctor in the Photo" seemed perfectly logical to us! On behalf of the audience, we appreciate the effort.
Source: Digital Spy