We've seen this problem arise many times... as far as fixing it, the best solution is try to get a Heroes Charge mod to come here and fix it. For anyone reading this that hasn't had this problem yet...I will say this once again...
DO NOT RECRUIT EZE UNTIL YOU HAVE RECRUITED MULAN.
DO NOT RECRUIT EZE UNTIL YOU HAVE RECRUITED MULAN.
DO NOT RECRUIT EZE UNTIL YOU HAVE RECRUITED MULAN.

Get the point? Yes it's a bug...and it's fine to recruit ezekiel first, as long as you NEVER, EVER, EVER recruit mulan after. Mulan gives you first sub. Eze gets you second sub. When you beat eze then go back and recruit mulan, you literally get first sub. Bad programming? Yes. We've known this for a long time. If anyone that hasn't lost 2nd sub reads this.... either you have recruited Mulan, or you never should.