The Morse code Carter sends to Jo and Taggart does not say "Crack Pipe".
When Taggart goes to pull on the manhole cover, it bends, clearly not iron or steel.
When Fargo rushes the door trying to get Jo's attention, he leans on it and it gives, showing that it's not the "sealed" door that it's supposed to be.
How is S.A.R.A.H. structured? There is an above ground entrance to the bunker. This leads down a flight of stairs to the main door. This door is on the downstairs level. There is a skylight in the ceiling with an escape ladder. In the centre of the living area is a flight of stairs leading up to the bedrooms.