We have project for channel earth works as a sub contractor,we finished the excavations,trimming and compaction for side slopes. All the work has been done according to the drawings and accepted by consultant. The inspections was for FDT and surveying works. I found some acceptable differences according to specifications for the surveying works (tolerance) of bed preparation (5mm - 15mm) The channel lining with concrete for 75mm. The contraction engr. of main contractor didn't accept the works while the works was approved,Most of the repair were to correct faulty level by Subcontractor, yet back charges were applied on subcon. without prior notice.
You should send a detailed letter to the Contractor disputing the back charges and explaining why they are not warranted under the subcontract. You should include the technical argument as to why your work complied with the plans and specs, as well as making the point that you had no opportunity to correct any issues with the work.