Problem with a lender or other company charging your account: Checking or savings account

I disputed a charge made to granite depot because they canceled the contract, did not install any countertops, and want to keep part of my money that was paid. My bank ( Wells Fargo ) sided with them on the dispute and would not give me my money back. The facts are simple. I did not agree to any charges other than for countertops, which is clearly stated in the contract. I did not agree to the charge for templating $350.00 and an admin fee of $39.00. These fees were not even discussed in the contract so Im confused why my bank did not refund the money. And granite depot also were going to make me sign a document saying I would not talk about the situation.