Can they set off contra-charges against my final account?

Only within the contract's set-off rules and the notice rules of the Construction Act, and charges invented late often fail both tests. Set-off means the payer deducting its own counter-claims from what it otherwise owes you, and contra-charges are the specific costs it says you caused, for example putting right defects or the cost of finishing late. A set-off is a claim like any other: it needs a proper basis in the contract or in law, records that show the cost was incurred and genuinely caused by you, and, crucially, where it reduces a payment that would otherwise be due, a Pay Less Notice (the formal notice under the Construction Act 1996 that a payer must serve by a deadline to justify paying less than the applied amount) served in time. Miss that notice and the deduction usually cannot be made for that payment cycle, whatever its underlying merit. Schedules of contra-charges that appear for the first time at the final account, having never been raised while the job was running, tend to be negotiating documents rather than proven costs, so take them apart charge by charge, testing the basis, the causation and the notice for each, rather than haggling over the headline total.

Picture a plastering subcontractor whose final account claims £46,000. When it applies, the main contractor responds with a schedule of contra-charges totalling £40,000, none of which was ever mentioned during the job: £15,000 for alleged defects, £12,000 for cleaning and £13,000 as a share of the project running late. Rather than argue about the £40,000 as a lump, the subcontractor takes it apart. The defects charge has no inspection records and no notice, so it fails on evidence and on the Pay Less Notice the Act required. The cleaning charge has no basis in the contract at all. The delay share is not shown to be caused by the plasterer rather than others on site. Charge by charge, most of the schedule collapses, and the £40,000 that looked frightening shrinks to a few thousand pounds that can actually be supported. Testing each line, not the headline, is what does the work.