Does it to be every now and then. I've noticed its more often with Sonya though.

It does it sometimes. I think what happens is the A.I. presses a certain command and it accidently sets off a Fatality move.
Sometimes when I fight Sub-Zero, the A.I. might press F,D,F,HP by accident and it automatically does that fatality.
This was fixed up in the later MK games.

Hello. I hope you have not encountered any fatalities since you posted, as it's been some time. I just wanted to point out that the CPU controlled character doesn't enter inputs via a virtual controller and "accidentally" mashes a fatality in. They control the craracter directly, and doing a fatality is basically more like generating a random number and then checking whether you won the fatality lottery or not. They always "know" how to do it. They're just programmed not to do it every time, to give the fatality more value.