There was a plan / understanding that they were going to build an underground station at Piccadilly and then they changed their mind. I doubt that was down to the geology.
What aspect of the geology makes it difficult? From what I can remember manchester is covered by glacial till deposits. There's a huge basalt erratic that is the quadrangle of the University of Manchester which was carried down from the Lake District and discovered in construction. Then of course there's coal measures. Whatever problems there are haven't stopped them building mines, underground canals or foundations for the towers and they started work on the Piccadilly to Victoria underground.
