[SPOILERS] SOMA unsolved mysteries thread

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However, there is one thing that does make sense. If you assume that it was Carthage who created Simon, then an explanation comes to mind. That man was a Carthage operative, tasked with doing the preparations for Reed's body to accept Simon and initiating the scan. He would've been able to do everything necessary, including opening the security lock on the door to gain access and the locking up behind him to protect a confused Simon from being immediately killed. He then could've retreated to the robot bay and taken refuge in that spare room until he was either rescued or could find a way out - neither of which happened, as we know.

As I mentioned in the reddit thread regarding who made Simon 2, the Omnitool room was locked from the outside by a human.

This leaves two possibilities I can think of, either the person in the Omnitool room locked it from the outside, then entered again from the vents. Or another Carthage agent locked them inside (maybe for their protection, maybe not).