The easiest way to avoid this problem is to equip your gals before the mission using the inventory button on the craft equip screen. After equipping all of your soldiers with your preferred loadout, hit CTRL+ALT+X to remove any items not currently being worn by a unit. Then manually add whatever items you might need in case of an emergency or a "surprise" encounter like zombies or whatever.
It's a pain, I know, but using saved loadouts helps. Doing this also helps with mitigating the loss from having your main transport being shot down by hunter-killers.