Under an NEC3 ECC main option A, the required warranties would likely be included as an activity on the Activity Schedule. Payment of these would be dependent upon completion of the relevant activity, as determined by the definition of Price for Work Done to Date. If the warranty requirements have been included with other work in a 'combined' activity then they wouldn't be paid for until the 'combined' activity work is completed.
If a warranty is required then it could be included as part of the Works Information requirements, which determines what the Contractor is to do and describes any constraints on how they do something. Alternatively it may be included as an additional condition of contract 'z-clause'. Under NEC4 this issue is now dealt with under secondary option X8.
For main options C, D or E the cost of warranties is treated as included in the Fee, as there is no cost component in the SCC which provides for this.
In direct answer to your question, there would be no need to retain monies as payment would not be due until the associated activity is completed.
If a warranty is required then it could be included as part of the Works Information requirements, which determines what the Contractor is to do and describes any constraints on how they do something. Alternatively it may be included as an additional condition of contract 'z-clause'. Under NEC4 this issue is now dealt with under secondary option X8.
For main options C, D or E the cost of warranties is treated as included in the Fee, as there is no cost component in the SCC which provides for this.
In direct answer to your question, there would be no need to retain monies as payment would not be due until the associated activity is completed.