I can't give you an explanation as to why, but I wouldn't worry about it.
It is just a cable guide under very low load so as long as it seems well secured it should be fine.
On any with protruding stems, use a small cut-off disk in a dremal to remove the protrusion and then grind it down flush to the rivet head. It will be undetectable when painted other than some will have holes in them.
You can fill the holes on the ones where they pulled out, with a small amount of sandable filler if you want them to all look the same. A lot of builders do this for all of the blind rivets anyway.