Got to the point where I need to "continue working with Father" in "Underground Undercover." Go to the house in "Pinned." Kill the gunners & the brotherhood - now it's just 3 Minutemen standing around. Apparently I am supposed to be able to hear them talking about their plan to attack, but they are not.

I am unable to initiate conversation with them. The three of them are all marked with green quest markers, and I am supposed to "take care of them." The guy inside the house won't talk to me, just keeps saying I need to take care of the threat outside.

I've tried leaving and returning, tried talking to the three Minutemen again and again, I've even tried killing them but that turns the Minutemen in general against me.

Read under Detailed walkthrough

http://fallout.wikia.com/wiki/Pinned

You have three choices!

Yes, thank you, I am aware of the choices. I also watched a video showing the situation played out. I WANT to talk to the Minutemen and convince them to stand down, but they WILL NOT talk to me. They just give me the basic NPC responses rather then engaging me in the quest.

Reload and do that quest again! (preferable load a save before you got that quest, do get it again)

Ok, it's just annoying as I've done a lot of things in between before realizing it was broken. Setting up a new settlement, crafting, exploring and the like. Oh well...