There is no confusion. If the inspecting staff marked it as not done, take it as not done. No contradiction, please.
Role of Subcontractors in Construction
Subcontractors work in the name of the tender-participated and tender-approved main contractor. Even in an additional agreement with the principal employer, the main contractor declares who his subcontractors are. In some field works on the worksite, many subcontractors, unnotified, also complete the given contract work. So, nothing new... only the pretense of the main contractor not knowing anything about his subcontractors more than he found in the work field.
Challenges in Construction Work
It's an open secret. Some engaged engineers cannot by themselves complete the obtained tender work. Construction work is always completed by building construction workers only. All their wages are legal, and they are not unpaid waged workers. They are all authenticated workers of the main contractor through subcontractors, like a small number of engineers.
Compliance and Legal Obligations
There is no escape from maintaining all such registers and records and providing insurance scheme memberships, safety precautions, and ambulance medical aids as per the number of workers engaged. The BOCWW Act clearly mentions following at least the main features like wages of construction workers, safety insurance, and health conditions.
Take care of your normal workers on the construction site. All the best, sir.