Ok...so I went back to an older save to try a few different things and I think I might be stuck now...or just missing something obvious.
I'm on the quest "You and what army"
Benny is dead
Caesar is dead
House is dead
Yes Man has gone to the Lucky 38, and I talked to him there and got the demonstration of the upgraded bots
He is saying to go explore the bunker at the fort.

I can get down the stair case (I previously had opened it before killing Caesar with the chip, but never went down inside)
Can get through the first door
Yes Man's face is on the giant monitor
The door in that room though won't open and just tells me I need to have a key.

So what am I missing here...or can I not get in there now for some reason?

I think you mass it up by killing Caesar while you should have go inside.......

Yes Man's face is on the monitor. Okay, now have you tried talking to him?

Yeah, he doesn't respond.
There actually isn't even an option to click on it.

Most likely a glitch, there's also another one that breaks the main quest if you turn the platinum chip in to Mr. House before activating the robot army...he sends you to activate the army but doesn't give you the chip to actually enter the bunker so you get stuck. You may have hit a similar block.

Yeah...It "feels" like I should be able to talk to the Yes Man on the monitor and get him to open the door, like Mr. House does at this same point.
Oh well...first really big glitch I've hit and not surprised, New Vegas has quite the tangled web of quests.