Spoiler:
On the car not being planted by the cops: What about when that one guy was on the stand and they play the recording of him running the cars plates and he says, "99 Rav-4?" "Yeah" and his eyes go as big as the sun. He was looking at the car days before it was found on the Avery property. He thought that info was supplied by dispatch but it was supplied by him.

On the bones, the one expert testimony pretty much nails it - when the bones are moved, the majority of the bones are found at the place they were moved to - not the other way around. Why are there a few bone fragments at that other location in the quarry?