I don't know if it's a real bug or some temporary oddity or some gameplay stuff i'm unaware.
My assault squads fly on a Scorpion, so when they land i can have a good idea if i can take the mission or should just run away as some enemies are spawned close to the ship.
Except that time in which i was basically in the unknown as i was facing enemies that i had never faced before, so i deployed all the gals on the ground and battled through the map for a while and in the UFO i started to notice some specific enemies that i think my Gals weren't equipped to defeat at that point of my game.
So i called everyone back to the Scorpion with some quickly grabbed loot, and when i used the emergency retreat button it was always telling me that i had Gals outside, when clearly all of them were in the Scorpion, after a lot of trial and error in moving the gals around (always inside the Scorpion) i finally managed to not have that warning anymore and could then get away without leaving anyone.