A diagnostic fee is normal, it is so you don't end up having them spend time on your vehicle finding out what is wrong with it, and then for you to take it somewhere else to get it fixed. Any reputable shop will have it, not just dealers, and it is usually waved if you have the vehicle repaired there.

You didn't say what is wrong with them but brakes are a wearable item, so CPO or not, it is your responsibility. If it is pads and/or rotors, do it yourself to save a bunch of $$$.

As far as CPO, you'll have to sort it out with the dealer and/or find out if the vehicle was indeed a CPO vehicle when you bought it. Dealing with these headaches is why I don't like CPOs and prefer 3rd party warranties, so I can take my vehicle where I chose and not where I am told.