The CPO agreement makes the limitations and charges very clear, you should have read the agreement before you complain to BMW or the dealer.
The very first thing in the contract is
"There is a $50.00 handling charge (per repair visit) that must be paid by the customer for any repairs covered under the terms of the Certified Pre-Owned BMW Limited Warranty."
I don't mean to sound unsympathetic but BMW makes you sign a document that has all this information on it.
http://www.bmwusa.com/Standard/Conte...tDg997SwxWlR3E