NEC ECC: Missing item in Accepted Programme

If an item is missing in an Accepted Programme now that PM and Contractor realise there is an error on it. Can PM using clause 32.1 to instruct the Contractor to submit a revised programme?

Absolutely - exactly what that clause is there for. The Contractor then has to submit a revised programme within the period of reply for acceptance correcting the known mistake, otherwise that programme will not be accepted.