You were duped on tire tread depth? Just look at your tread wear indicators and if they are flush with the top of the tread they are done. As far as the lug nuts, that's a good reason to bitch.

My doctor drives a Cayman and when in for an oil change they also changed his wiper blades at a cost of almost $150. Thing was, he had just changed them himself. He asked them to put his old ones back on. They said they threw the old ones away. Anyway, long story short he refused to pay for the new ones and the dealer finally relented. I had a BMW and was surprised how many things they assumed you wanted done without asking. Perils of owning a Premium vehicle.

Unless you agreed in advance to having the work done (usually by signing the work estimate), you don't have to pay for "extras" like that. Doesn't matter what the dealer says or how mad they get.