You are not specific as to what these additional costs are. However in the NEC any contra charge would be subject to the Notice of Intention to Pay Less (Y2.3) HGCR Act 96. You have to have a basis under the contract to payless stating the reasons e.g. a breach of contract which has caused the E to incur additional costs. You must also give the required notices as required.
Generally the recovery of losses to the Employer form the Contractors non performance will come from delay damages X7, assessment of the cost incurred b y the E for the C not providing things he is to provide in the WI (25.2), assessment of E's additional costs of the Contractor, missing a Key Date (25.3), repeating tests and inspections (40.6), uncorrected Defects (45.1).
Generally the recovery of losses to the Employer form the Contractors non performance will come from delay damages X7, assessment of the cost incurred b y the E for the C not providing things he is to provide in the WI (25.2), assessment of E's additional costs of the Contractor, missing a Key Date (25.3), repeating tests and inspections (40.6), uncorrected Defects (45.1).