Can the dealer charge fees if the vehicle is under warranty?

I have 2 issues with my 2009 Toyota Corolla. It makes a grinding noise for a couple of seconds on a cold start up and its leaking coolant from the water pump.
Both problems are covered under the power train warranty and Technical service Bulletins were issues to Toyota for both problems so they are aware. I recorded the noise my car was making with my phone because it happens intermittently. I've never had the "pleasure" of taking my car to the dealership and I'm a bit unsettled. My question is could the dealership charge me for any other fees even though both problems are under warranty? I feel like I'll be walking into a Lion's den. Any tips would be appreicated, Thanks!