I supposed that Muni could take liquidated damages for the difference in the life expectancy of the rail, and the early replacement costs, if it is not a safety issue.

IIRC this is what MTA ended up settling with Breda for, when they delivered the "pigs", with excess weight significantly over the bid specification. IIRC they settled for the additional expected electric consumption and track maintenance.

I've seen well run projects public and private, and very poor ones. I have also seen a vast majority of these screw ups. There are ways to prevent them with competent experience staff who are able to write good specs, good contracts, and act with due diligence providing proper oversight, both on the part of agency staff and contractors. Inexperience, stupidity, lack of good approval processes, plans, specification, or financial controls, and excessive political interference in the contracting processes, can and do screw things up.

Unfortunately, there is often no learning curve with these screw ups, since there are few penalties ever applied, and these "make work" screw ups mean another "change order", and more billable hours or contract markups, doing it over........perversely rewarding the bad outcome, with more of our money.......