It looks like the Contractor requested you to provide a quotation for a proposed CE, which would be assessed in the same way as an instructed CE, including risk allowances, where appropriate. There is no separate requirement for you to be instructed to include this as it is part of the assessment process under clause 63.
To my mind, however, the main issue here is whether the supervision services were stated as being part of your 'scope' requirements and whether you actually provided these. It seems that the Contractor has linked the 'error' made by the specialist supplier installation team with an assessment under clause 25.2, however, this clause is specific to 'not providing' any stated services, rather than the manner in which they were provided. If a Defect occurred then this is dealt with under the corresponding, separate procedure under the contract.
As much as the Contractor may feel justified in applying this 'contra charge', it appears that they have linked the matter to clause 25.2 'for convenience', rather than having any genuine entitlement.