I can't say much on the science end of things, but one thing I do know about Bones is that the writers decided not to write Bones as being on the autism spectrum, just very focuses and drastically out of touch with pop culture, whereas the actress who plays Bones apparently did a lot of googling or something and decided to play her as being on the autism spectrum, against what the writers had decided. This came from an interview the actress gave, and I didn't get the sense that she did a lot of in-depth reading before making that particular character decision; that probably accounts for a lot of the more drastic discrepancies right there. (Not all of them, of course; sometimes the writing, especially in the last few seasons, can be really uneven. But some of them.)