Reading the strategy guide might also give you some idea of where things are going wrong. A staff member has been cloned, or part of a room flashes randomly between patients and staff. Other random items appear in this place when the doctor is sacked and has left the hospital. When I restore a game saved during a bonus level I get the first level again. This is a bug, restore from your last saved game.
Queues are too long, and patients are leaving.
At peak time your queues will be long anyway, place your best doctors in the key rooms that have bottlenecks. Add an extra room of this type to the local area to help balance the load. Redirect patients to a quieter room in another part of the hospital. Clean up the local area by dropping in a few handymen. Bump unhappy patients to the front, particularly ones that are close to being cured.