Its not just one stack that fails to generate mate, its every single rebel stack (all should be spawned directly into rebel-controlled settlements). The end result is 'empty' rebel settlements that other factions simply conquer by moving their army stacks (which generate with no problems) into the settlement. The rebels can still train units, but its the absence of any starting stacks that is the problem.

May be something to do with the fact that the rebels use the Roman culture type, even though they can take advantage of all 6 cultures' building / recruitment rosters. The puzzling thing is, in BI the rebel stacks generate fine.