Firstly the parties need to establish if there is a Defect or not, as the Employer designed the works it could be defective design rather than defective construction. The Supervisor should instruct the Contractor to search under clause 42.1 (assuming NEC3 ECC) if a Contractor’s Defect is found then usually the Supervisor would notify this as a Defect and the Contractor should rectify it. This doesn’t sounds like a major issue so it probably wouldn’t prevent Completion being achieved, in which case the Contractor would have to correct it within the defect correction period after Completion.
If it was discovered that the cause of the settlement was defective design then the Project Manager should issue an instruction under clause 14.3 with a revised design detail that will rectify the problem. The Contractor should then implement this instruction and would be entitled to a compensation event under clause 60.1(10) as no Defect was found and also under clause 60.1(1) for changing the Works Information i.e. issuing new design detail.