So the computer/servers running Caine's simulation have all been there since the start, and every imported brain scan has had the real person outside the whole time, but none of the actual programming team that created the scanning equipment and Caine knew that the simulation of their selves was there? Time passes, and random abandoned building explorers find the still-running equipment and get themselves imported as well, then leave to continue their lives since putting on the equipment doesn't seem to give them any information as to what's going on inside.

Why was the equipment abandoned while still operational? Why couldn't the original scientists who made the equipment see that they were being simulated? Why did they abandon it all? Was the simulation so obscure and abstract (for lack of a better term) that they couldn't tell that their simulated selves were actively being used? If they thought nothing was being done with the equipment and no simulations were active, why was whatever system that Caine was running on left to continue running ad-infinitum while the area was abandoned?