I think the report is partially it. I think the items not being logged as separate items or tested by forensics are the main reasons. The phone obviously was not connected to the headphones any longer and it was not in TM's pockets or on his person, so it was bagged separately. I would think the headphones if on the ground around the body would have been bagged separately from items found within TM's pockets.
Again, I don't think the defense has focused that much on this issue as its not practical for them and not as important as other pieces of evidence. Even if they could somehow prove that those items were collected from TM's pockets from detectives, the state would just say other police put them there after the fact and there isn't any way the defense wouldn't have anyway to disprove it.