I have this issue on a multiplayer server I play. Magazines cost in-game currency and this has to be one of the most frustrating issues, that and the naked bug. I'm unsure what causes this issue however it seems to happen more often if not exclusively with non-full magazines. It can also happen when you're moving stuff in and out of a vehicle. I assume the reason this hasn't been fixed or looked into is because you can't reliably reproduce it.