OK - this seems to be a small bug :-)
I managed to reproduce it (after several attempts) on a simple Battle - chose the Small Scout, minimum Tech, Sectoid and tried several times. When the randomized item set is the one with the pistol - I get a repro (no mind probe). When one of the other sets is chosen (Rifle or H.Plasma) - the mind probe is there all right.
Seems to be a problem inside the AddItem() in BattleUnit.cpp, but I am seeing the code for the first time and not quite figuring out the logic yet. Hope that someone smarter would notice where the problem is :-)