There are a few locations in the game that I've passed through repeatedly, and yet I haven't "discovered" them. In each case, it seems to stem from an NPC telling me about that location and adding it to my map. And no matter how many times I walk through and over that area, I never discover it and can't fast travel to it in the future. And now a quest isn't working because I haven't discovered the area.

I am playing with some mods, so that may be causing the issue. I'm curious if I can use a console command to force discovery of the location.

It probably has something to do with the scripts.I really cant help you in anyway other than that because its never happened to me.

Some of those locations are only discovered when you pass through an exact spot. A good example is East Pump station, where you need to jump the pipes between the pump station & cistern before it registers as being discovered. I've managed to have all locations as being discovered in the map so I don't necessarily think it's that kind of bug as you state, but is another kind of bug, where the proximity of the trigger is set wrongly.

Anyway the console command is tmm 1