I don't think this is a problem with the game, it's more of a problem of me not being able to figure this out, but how do you change weapon slots?
The fourth weapon isn't assigned to anything by default, so once you put it down, it's gone. Using the switch to previous/next weapon keys doesn't switch weapons at all, the "arsenal" in the journal doesn't seem to let you change anything, and there isn't any slots in the customize controls options to change them. I figured out weapon 1 is 1, 2 is 2, and 3 is 5. I've blown up fletchettes in my face clunking around to find that 4th weapon key.