Large units in UFO
In X-COM UFO, Reapers, Sectopods and Cyberdiscs are 2x2 squares big. If you mind control them, you'll mind control only one square which will become hostile against other parts of the alien and may even attempt to attack them via reaction fire. Control all four sections, and they'll not try to shoot themselves.
Large units in TFTD
In TFTD the Triscene, Xarquid, and Hallucinoid are the 2x2 units. In an attempt to correct the partial control bug in UFO, a host of new odd bugs related to mind controlling large units are introduced.
To fix the problem, the solution was to automatically mind control the next 3 units that come immediately after the controlled section. This in theory works perfectly as long as the primary quarter of the large unit is mind controlled. The programmers unfortunately did not take into account that players will launch an attack on any one of of the four quarters of the large unit. When this happens, the large unit will be partially controlled clockwise from the location that was controlled, while the rest going anti-clockwise towards the main quarter will be left untouched. This results in a partially controlled units.
To make it worse, when control is returned to the aliens on the next turn, the game will flip the ownership flag of the large unit from the point that you controlled the unit. Since the game is expecting to flip four sections where you may have only partially controlled less than the four sections, the flag flipping may spill over into the next unit in the unit list. By the start of your turn, you may suddenly find that you've gain permanent partial control of a completely unrelated large unit.