When Shadowspire enters the control room and Lyla hands over her sidearm the inlet valve in the magazine is visible giving away the fact her prop weapon is actually an Airsoft style pistol.
It is highly unlikely that an agency with security as strict as ARGUS would ever allow an agent who was confirmed dead to have the security clearance to access a command facility - especially if such access required a retinal scan and the aforementioned corpse was missing an eyeball.