There were FIVE cartridges total in Baxter's gun, INCLUDING the fired one. So the crook fires a cartridge into Baxter's head, puts the other five in Baxter's gun, and fires one of those into the ground or other backstop somewhere it won't be noticed. The result is that Baxter's gun contains a spent casing which was fired in it, even though that casing is not associated with the fatal shot.
And there were six cartridges total in the glaser pack - one of which was never found.