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.

There are reports that this can also happen when the unit does a gesture partway through a reload. (See: Arma Discord > arma3_feedback_tracker)

Intressting about it is the mag appears for a moment in the inventory and gets "deleted". Can happen moving mags from the weapon into a container too.

https://www.youtube.com/watch?v=kEiVquzS-mM

This is not resolved as of version 2.18

This issue has gotten worse in 2.18, was never something that I noticed happening before but now I can easily reproduce it on multiple different servers.
Does not occur in singleplayer from what I've noticed.

EDIT:
Seems to be fixed when client and server both are running profiling branch.

In T142540#2681526, @donniepcgames wrote:

This is not resolved as of version 2.18

Can confirm. Since 2.18 it happens a LOT in multiplayer.

This is fixed. But it would still be broken if a player joins your server using the old Arma version who has disabled automatic updates.
So to fully protect against this, you need to set minBuild in your server.cfg to 152405