After shooting all the shells, the reload sequence loads 6 shells into the tube, then pumps the action to chamber a shell. When top off loading after only firing one or a few shells but not completely emptying the gun, a pump action is still done even when a shell is still chambered.
I recommend removing the pump animation/sequence when the shotgun is loaded with at least 1 round still in the gun.
(Edit)
This also occurs for many other weapons in the game such as the BAR.