-The artificial horizon is inverted, pitching up will result in the horizon displaying a negative angle, and vice versa. This applies to the main horizon and climb/dive indicator in the pilot seat, as well as the horizon in the gunners seat. This image was taken while climbing.

-Both compasses in the Gunners seat display direction incorrectly. E.G. if you were to turn northwest, the compasses will show northeast.

-The night-time cockpit lights in the pilot seat obscure frontal vision, the high reflectivity of the interior glass will make seeing forward out of the cockpit very hard for the pilot.

-I'm sure this has been mentioned, but the tail hook on the F4 Phantom does not reset after being used.

-Using the pylon editor to give the Phantom three gun-pods, will result in the central gun-pod to not function alongside the other two.

-The pilot cannot obtain radar locks through cycling targets (R default) with the Sparrow or Sidewinder missiles (Yes, my radar is on). They can lock with T using the sidewinders and sparrows, although sometimes this doesn't work either, I do not know the circumstances that lead to this.
The Gunner however, can use these cycle target capabilities if they are given control of the AA missiles through editing pylons, with either sparrows or sidewinders, and it works 100% of the time. I tag this on the end as I'm unsure whether it's intended.