I am not about to try to reproduce this, because in both cases, I am down to my last magazine.
All inventory slots were full when these instances occurred - full backpack, vest, jacket and pants.
Scenario 1:
A. Take out pistol (via hot key), and shoot zombies until you need to reload (pistol and additional mags are contained in protector case)
B. Take out magazine and place on the ground, to try to reload
C. Magazine disappears
Scenario 2:
A. Take out pistol (via hot key), and shoot zombies until you need to reload. (Pistol and additional mags are contained in protector case)
B. "Reload" icon (clip icon) appears on screen when pistol is empty
C. Press "R" to reload or choose the option from on-screen menu
D. Pistol loads new magazine from inventory, but the empty one is not returned to inventory, and disappears.