In the final mission; The Aeon commander asks Fletcher for help at which point he gives some speech about how Aeon and Cybran suck and is at that point meant to go hostile. A cutscene should trigger over the water showing him turning on us and then the battlefield should extend.
However what seems to happen on two attempts since the recent patch is Fletcher will give his speech but the cutscene won't trigger, he doesn't actually turn hostile and the battlefield does not extend. A few mins later his units will start to enter the still small battlefield and are still showing as allied.
I have attached 3 game logs from 3 players.