The capacity of the Alliance fort is determined by the size of the rally of the first player who sends their troops to the Fort.

To increase this capacity, the first player sending his troops to the Fortress must upgrade the combat hall in his base to increase his rally size; afterward, the player needs to withdraw his troops from the Alliance Fortress and send them again to apply the new size.
Or a different player with a larger rally size can put his troops in the Alliance Fortress first.