Picking up a new gun / flashlight replaces the gun currently occupying that spot, which then vanishes
This has happened to me twice. I picked up a flashlight, which replaced the pistol I had in that slot, and the pistol vanished. It was not on the ground or in my inventory. I now had no weapon.
The second time, I had a crossbow equipped, and picked up a Lee. The Lee replaced the crossbow, which then vanished and was not on the ground or in my inventory. That was regrettable considering how loud the Lee apparently is.
Updated by GROM64 about 4 years ago
I just wanted to add that, this happens when you use option "Take..." in action menu.
If you use "Gear" option and manually remove/transfer old weapon from inventory, it removes that weapon along with all magazines and leaves it on the ground.
Then you can transfer new weapon to your inventory.
But if if you have a miss-click and use "Take ..." from action menu,
old weapon and all ammo for it in your inventory is gone forever :(