I have had this problem periodically since BL3 released. I’m looking at the map and sometimes when I try to add a custom waypoint nothing happens. It’s bothersome but usually closing the map and opening it again fixes it.
Now today it just no longer works. I can open and close the map. Nothing. I tried fast travelling. Nothing. I quit to main menu and came back into the game. Still nothing. Not sure if this is related to the specific map but it’s on Ashfall Peaks. Will try some other maps as well.