Backpacks, when Gathering is used and it is set to ALL on any page, and you use the /Remove command on your remove tool - Items in the Hot Bar will end up moving to the backpack page with the setting to ALL.  It happens only on items that would drop into an empty spot on your hotbar, when picking them up, such as a Gun or Box (but not ammo that was placed in the hot bar, as I tested)

Not sure which Plugin is at fault.  For now, I have turned off the Gathering ALL selection until out in the world collecting loot.