I don't know what starts with a C, but I know for a fact some horses can get injected with things and have complications one of which is muscle wasting.

A fellow board member here owns a horse with chronic muscle wasting, because of a bad reaction to a strangles shot and then steroid injections.
Which causes the horse to be skinny. 
If it is not managed carefully, it could easily produce a skeletal horse.

I don't think I would jump to conclusions until I had all the facts.
Find out what the horse has first.
If you don't trust your BO to screen out horses that could have an ill affect on the herd, maybe you need a new barn.