The First Evil was deliberately confusing the construction crews with a mixture of illusions and magic:
INT. HIGH SCHOOL BASEMENT - DAY
Xander and Buffy make their way through the maze of the basement.
XANDER: You can't use the blueprints to find your way around, down
here. Seems like the walls move or something...
Buffy: Same Time, Same Place
Note that Xander did indeed attempt to use his influence (as Senior Contractor) to have the Hellmouth covered in tons and tons of cement, but apparently he missed.
Xander: I got two crews working this diabolical yet lucrative new campus:
finishing up the science building here, and reinforcing the gym. No
pentagrams, no secret passageways... everything up to code and safe as
houses. I've looked through all the plans, I've been on site after