In the game end menu, it told me I had contained 106, even though I never actually even found his containment cell. This leads me to believe that the MTF's contained him, so a possible bug is the MTF's containing 106 results in the game in menu giving you the 'achievement.'

Locking since many of these bugs were fixed in v0.9.3. If you have to report any other bug for 0.9.3, then make a separate thread.