For reasons unknown players are unable to spawn a Droideka on Mustifar CTF for the CW era. It seems unfair (to me at least) that the Republic can spawn both special classes (Clone Commanders and Jet Troopers) but the CIS can only spawn one (Magnagaurd).
This is a limitation in the game that I have not been able to reverse. I know I can switch the classes around (via MERC-J's classes) and spawn Droidekas but then there would be no Magnagaurds and the Republic would still have all their classes.
This would probably be in the mission file but this may be one of the values that defaults from the disk and cannot be changed.