Design of Equipment is the Contractor’s responsibility and the Contractor is implementing temporary works at site without submitting to the Project Manager his design for the Project Manager to accept.
Firstly, the Contractor need only submit details of design for items of Equipment if the Project Manager isntructs him to do this.
Even if you did give such an instruction, looking down the list of Disallowed Costs in clause 11.2 (25) I do not see a heading which matches this for disallowing costs.
Short of going through each one, the third main bullet point seems most likely, but from what you have said, does not apply as (a) it is not an acceptance procedure stated in the Works Information and (b) you have not indicated that any additional Defined Cost has been incurred.
Assuming an unamended NEC main Option C - the ultimate sanction on the Contractor here is that he may well be late and miss the Completion Date due to his own inefficiency and so will incur delay damages if secondary Option X7 is used. If a Contractor is just inefficient (not being one of the Disallowed Cost items in 11.2(25)) then this is a shared risk.