Nope, it only happens when you've got a "Carry more ammo for <weapon type>" perk. Otherwise you don't lose anything. I've done a fair bit of testing. If it was intended you'd always lose it.. plus it would make the game, especially the raid, stupidly annoying. You wouldn't be able to run around and test out new strategies etc.. time you're done nobody has any ammo left. And considering the bug essentially removes the perk and in fact does the OPPOSITE of it, I very much doubt it's by design.