Exactly the opposite, I think it is the dealer that is being greedy and trying to take advantage of you. I wouldn't feel an obligation to pay anything. They had the opportunity and presumably did inspect your trade prior to agreeing to the deal. It isn't like you hid the condition of the upholstery from them.
However, if you feel like you agreed to help out, I would cite the new tires/battery and tell them you will give them $500. Unless you agreed to a specific amount in the contract, you have no obligation for a minimum amount. For me, it would be a take it or leave it kind of offer.