I believe you are correct in thinking that these items should only be tradeable without an item inside the nest. I checked in game and found that all uncrushed nests, whether they have an item or not are tradeable between players and shops. According to the wiki, nests crushed or not are tradeable, but when they have an item inside the nest as you stated, they should not be tradeable.
I'll issue this to the developers to fix. Thanks for the report!
EDIT : Reference: blitz/herblore#13