Hello NQuaday,

That's certainly a wierd error that they are missing. Were there large rebel armies there in Mexico or just small garrisons in the cities?

To be able to play as the Aztecs there's an easy mod
https://forums.totalwar.org/vb/showthread.php?t=72291

The only difficulties are moving troops over from Mexico via Merc Carracks and the complete lack of any cavalry/artillery/buildings/agents. You'd think in Europe they should at least be able to hire some Hobilars or Scouts and ballistas.. I got around these problems by judicious use of the move and create character cheats. Also be careful to protect your general, they drop like flies when hit by cav.

Best of luck sacrificing some pagans (re: catholics).