[Edited by Sunbeam, 8/5/2010 6:19:55 PM]
When on certain missions with options 8 & 9 on, you cannot destroy the mini-boss - eg you cannot destroy the purifier mothership in Haven mission.
Any solution to this besides turning off the trainer
Use the option to take control of the mini-boss unit. Turn off invincibility. Turn off super damage. Use your own units to then kill the mini-boss unit.