First of all i just want to say hi to the community, this is a hellova game.
Anyways, back to business. I am having the same problem with the empty inventory bug like many others. But for some reason I equipped four normal rifles on a squad, sent them out to fight of some aliens.
When they returned I went to replenish their ammo and for some reason I had more weaponry in the store and incidentally these are the very same weapons that disappear when in game.
Just thought you would like to know.