The man inspecting the lock concludes:
"Door wasn't forced, lock wasn't picked, as far as I can tell they
basically just walked right in."
In saying that, it's not clear that he concludes the door was left open. It just implies that the prisoners either had access to a key or that the door was not locked.
The infirmary staff member who is in the room at the time exclaims (defensively):
"I don't see how that's possible, these doors are locked down every
night when we leave - it's priority number 1. Only thing I can think
is... someone left it open for them."
It certainly seems he is implying that somebody left it open on purpose, but it's possible he meant that somebody forgot to lock it or let them inside. I think in the moment he is just trying to avoid any blame being pointed towards him and those words come out (a similar thing happens with Katie when warden threatens her; she immediately mentions Sara's relationship with Michael to protect herself by taking the focus off of her).
You should also take into account that the lock on that door was changed the day before, so maybe he didn't think it was possible for somebody to duplicate a key in that time.
I find it even stranger they didn't consider the use of the guard's keys (the one who was guarding Lincoln). It's impossible to know for sure, but you would think he had keys to access all areas (considering he was in the infirmary area alone anyway) and they knocked him out...