This happens with all ammo types, I notice it especially when unloading a mag.

I'm finding this also. However I seem to have narrowed it down to when the game needs to create a bullet "icon" (i'm not sure what to call it, but the bullet icons that can have a certain quantity to them before another is needed).

For example, if you have a 9mm bullet icon in your inventory, and lets say a quantity of 10, you can empty a mag until it reaches 25 which is the max for the 9mm bullet icon. Then normally it'd need to create a new icon and keep going. However now you just lose any additional bullets from the magazine.

And if you don't have any icon of the bullet you're unloading from a magazine, you lose all of them.

Also the same happens if you're unloaded straight from a gun, not just from magazines.