I own a Pentax Super A, which is very similar to the ME Super - I think the Super A was the top of the ME line.
I have the same problem - some shots are underexposed.
When I checked more closely, I found that in aperture priority, when closing the lens slowly from f 2 down to f 16, the shutter speed selected by the camera would initially increase accordingly, but all of a sudden would 'jump' to a value that would lead to a 2 - 3 stop underexposure.
For example, I started with f2 and 1/250, then down to f 2.8 and 1/125, then f4 and f 1/60, then f 5.6 and 1/500!
I sent the camera to a repairer, who explained that a magnetic band inside the bajonet (you can see it when you look closely) has worn out, and that this is not reparable.
I since bought a second Super A body in the hope to get one to use for spare parts, but the problem is the same.
You can still safely use the camera in manual mode, and rely on an external exposure meter (or your experience).
Alternatively, as this error seems to happen mostly at medium f stops (like 5.6), I measure in manual mode at stop f 2.8, and then adjust time and aperture accordingly.
Other than that there seems no real cure....
sorry!
Ansgar