I'm gonna try to explain this situationally.
I had a MK II placed in my inventory higher than its' magazines. Whenever I used the mags up and reloaded, they would seemingly go back to those spaces where they were originally, but it would render those mags unreloadable and, when dropped, ungrabbable. When re-logging, the mags appeared in the space of where my MK2 was, and the mags worked perfectly well. Since then I've remembered to place my guns as low down in the inventory as possible, so my mags won't occupy the spaces of those guns they're used on.
This bug doesn't apply to mags which have their appropriate guns in their dedicated slots (Holsters and shoulders).
Game version: 1.07