I think they got reckless with their expansion. The San Jose location moved to a new location after their lease expired. They chose to relocate to a prime location in downtown San Jose and ended up with a million dollar shortfall to renovate and open the new location. They somehow managed to scrounge the money through an appeal to the community and opened but it must have ruined their financials.
At the same time they were opening in other cities. If their financials in the Bay area were shaky (as they admit in their closing statement on their website) then it is not clear why they were taking on more risk by expanding.