In the public 0.3 release, if you retreat from a dungeon with downed party members, some of them won't show up in other combats until you remove and put them back into the party, seems to happen to all but one of the downed members everytime so I'm guessing there's a missing or messed up 'for' loop on retreating.
Edit:
It turns out this happens occasionally if your party members die in normal fights as well, whether you retreat or not, it'll only revive one of the downed members sometimes and you need to remove and replace them in the party to fix this.