Complex sentence: The "discrepancy" is that each end, or abutment, doesn't count as a pier, though, were they to be counted, one would have the proper number of piers (12) for the 11 arches mentioned.
Split into simpler sentences: The "discrepancy" is that each end, or abutment, does not count as a pier. Were they to be counted, one would have the proper number of piers (12) for the 11 arches mentioned.