My house is in Florida Roofer didn't follow proposal. Left old underlayment and wanted to leave old wet rotten plywood as well. I did stop them and they replaced the plywood on the flat roof Didn't call for inspection so I did. Inspector found several code violations that had to get corrected before passing final inspection. Took 9 weeks for the roofers to correct it. Now they increased the bill by almost $5000dollars. I am willing to pay but only for what they did and not for their srew ups.
You should contact an attorney to determine what you should pay, or contact the roofer to attempt to negotiate directly with them.