Is the manager sinful for preventing an employee from praying in congregation in the company's prayer room, on the pretext that the prayer takes too long, and is it permissible for the employee to pray individually to avoid problems, and what is the ruling on his prayer and its reward?

The manager does not have the right to prevent you from praying in congregation, and he incurs sin if he does so. You are not obliged to obey him unless you fear that your livelihood and job will be harmed. In that case, you are permitted to miss the congregational prayer and pray individually, while searching for another job where you can fulfill your religious obligations.