They're inside a what??? (Spoilers)
I'm not sure how this got started, but it seems to be very popular theory about his movie- that they're inside a simulation or a computer program. There's absolutely NOTHING that indicates this:
-While trying to escape, Nic breaks through a PHYSICAL barrier. Nothing about him has changed on the other side, his artificial legs are still there etc. There are no signs of glitches to indicate a simulation or anything else of that nature- there are just lights bouncing off Nic from a distance.
-Those who champion this theory also seem to think that Damon is putting down the humans/programs that are malfunctioning because they are failed experiments. Again, there is NOTHING in the film to suggests this is true. It is explicitly stated (several times!) that those people are malfunctioning because they've been in contact or close proximity to Nic and his friends. When Nic is wheeled around the facility, the people in the suits are cleaning oil off the wall, not blood. So the other failed experiments were those that had rejected their mechanical augmentations. This is backed up by the fact that Damon is concerned about the substance coming out of Nic's nose, only to later remark "It's okay, it's just blood".
Unlike Nic, Jonah and Haley, none of the other people outside the facility had any markings, deformations, signs that they were experimented on, discarded or touched in any way. Everything points to the fact that while Nic, Jonah and Haley were experimented on inside the facility and allowed to escape, the people outside the facility (who were clearly older) were there to test how they reacted in close proximity to the test subjects.
This all points to a Truman Show like enclosure of an alien nature, and not a simulation or computer program. There's no reason for Damon to hide as a half android if this was a simulation, he could easily just pass himself off as human- it's just silly. If this was a simulation there'd also be no point in having the hazmat suits, which the EBE's use to protect themselves from the humans. Nothing the movie presents suggests otherwise, so there's no point in adding unnecessary layers that just aren't there.