Defeated susa 100% on the fertile crescent campaign and got an error message saying to restart the app during the payout screen. Restarted app and all of my army was gone (surviving troops were lost) and susa doesn't show as defeated on the map
In this case the attack was SP as opposed to MP, so indeed this extends to both realms of combat. Elijah, let us know if doing what Patrick suggested allows you to circumvent this bug (re: his thread on MP).
Do you recall anything about the error message, including any text description and/or error code(s)? This should help the developers track down the source(s) of the bug more quickly.