NEC 3 Option B: Is it correct for the supervisor to watch men carrying out works which he believes will lead too a defect, then record and take pictures without given any advise at the time. Then it is issued as a defect the next day?
This is not particularly in the spirit of the contract, but nothing contractually you can really do about it if this is the personality/character of an individual. At the end of the day your guys should make sure they are complying with all the standards and specifications whether the Supervisor is there or not. You should be self certifying your own work and not need someone else to tell you it is not correct.
Not withstanding that - this is not nice to hear going on. You would like any individual would at least warn the guys in their opinion that could lead to a defect even if they choose to ignore it. Unfortunately there are individuals out there in the industry who seem to get a kick out of a Contractor doing things wrong and I have met the odd one in my career, but thankfully those type of people are not common place.
It should not be in the Supervisors interest to allow defects to happen as that could delay Completion which even if there are delay damages is not what the Employer/Client wants.
Try and work on your relationship with this individual, or talk to the Project Manager about it and see if they can speak to them and change their ways. Otherwise just don’t do anything that they can pick you up on anyway!
I would add to Glenn’s comments if the informal discussion with the PM does not work: notify an early warning as about something which could affect the Contractor’s total cost (as well as delay Completion). Then have a risk reduction/early warning meeting to discuss but - as Glenn says - be open about your failings too as it is your obligation to do the works and not rely upon the Supervisor to point out Defects.