I entered a Citadel mission, defeated the scylla (paralyzed) and evacuated all soldiers. The first mission complete screen comes up with experience gains, however upon continuing it took me to the last autosave instead of the geoscape “mission won” screen.
I did go back and killed the scylla, with no change. The mission was a clear win, with lots of turns of paralyze. I have repeated it three times and can provide a save. I have the console enabled but have not used it on this save.
I cannot yet reproduce this (anyone?) but as soon as I reach citadel missions, will get you know. If there is such a bug, its a loop that is gamebreaker.
I have since played a citadel mission and completed it both ways with it working. It might have just been a glitch. If it happens again or someone else has it happen I will upload save files.
I reported this game stopper issue a few days ago via F10 doing “the crystal crossbow” mission. Hope that it will be fixed soon. It’s rollback, like Groundhog Day.