Some levels have key-cards to open locked doors that have an exit/entry symbol, just go near desks and computer terminals to get these or maybe in a locked room near desk. Some levels must kill all or most guards to get key-cards to exit level, then check all doors and look other exits such as vents at floor level or higher up near ceilings. Most have doors to exit level. Time-shift and check too.
Specific Harder Levels:
Vent area outside lab room at floor level leads to a secret and return back to lab room and garage door lift to exit.
Centre army battleground pit (after meet Mason) – return to pit near army swag tent when got rid off all guards and jump/fall in to exit.
Head to garage like wide door to exit (may need kill all guards 1st).
Speak to a prisoner man in corner room near security camera, then throw at hazard posts – guards will come – get rid all and continue hazard posts breaking until back red door opens. Also hidden vent near floor area of these rooms where can find a secret – may need to time-shift to see.
More guards in inner computer room -plenty large things throw and get rid all then push alarm button. Also a sapling tree have to take and move to previous area (hint: where was a pool water/liquid) to exit the level.
(The prisoner may escape later when you finish game -no further interaction).
There is a vent in a centre room area have to climb up from trolley/table to see and access. Then go till find another vent and drop down and do time-shift to get a clue and look on floor for something to use in the medical room. Easier to do once all guards killed off.
If door not opened go see if any guards trapped in a floor fan or other and make sure blast to kill off. There should be no guard communication voices once all killed.