If you believe your contractor is overcharging you, it'd be wise to review the contract and their invoices to identify where the overcharges are being made. And, providing a formal, written response to the contractor's billing could help to keep things above board and also generate documentation that could be valuable later on.
If it looks like the disagreement is heading to a full-on legal dispute, it might be wise to consult a local Arizona construction attorney. They'll be able to review the contract and invoices to determine whether you're being overcharged, and they can help with disputing those bills.