When reloading any type of gun with a detachable magazine, there are several features in the game that govern what happens.
#1: The player is able to find magazines and ammunition separately, then combine to have loaded mags. This amount of magazines is carried by the player in an inventory type system. When the player reloads his/her weapon (whether it is empty, partially full or full), the magazines in the inventory are cycled, replacing the mag that was just in the gun.
#2: There are 2 ways a weapon can be reloaded. The reload button can be tapped or held - tapping the reload button will result in the player dropping the magazine from the weapon and replacing it (one less mag in the inventory). If the reload button is held, the player replaces the in-gun magazine back into the inventory. Obviously tapping would take much less time than holding, but you would lose one of your magazines.
Of course you could always pick it up later
