The different position of the F-14A engine nozzles in the hangar isn't a bug, it's feature! In real life, F-14s with their engines off look the same.
When an engine is shut down, the one engine is turned off first to test the bidirectional pump, ensuring the flight hydraulics still work if that engine fails in flight. After this check, the flight hydraulics are turned off, so the one afterburner nozzle stays open due to no hydraulic power. Another engine continues to power the weight-on-wheels system until it is shut down. When said engine winds down and power is lost, its nozzle closes due to the loss of electrical power and leftover fuel pressure. This sequence leaves the engines in different positions: the one nozzle open and the other nozzle closed.
