OK, here it is:
I have two bases. 8 soldiers on one, two on another.
I got the base 2 attacked, after which I couldn't have soldiers on base 1 equipped anymore.
Whenever I go to equip screen, be that at any time via craft, or when a base gets attacked, I receive equip options only for the two soldiers on base 2. Now, where it gets even funnier is:
equipping them with whatever stuff actually equips that stuff to soldiers in slots 1 and 2 in base 1. Even if I don't have these weapons on base 1 at all