The project was regularly in the headlines for it remarkable cost overruns ($2.6 billion projected cost up to $14.8 billion) as well as some other problems, including leaking tunnels and most notably the death of a motorist from a falling concrete panel. That last incident was recently resolved with a settlement of $6 million between the family of the victim and Powers Fasteners, the company that manufactured the epoxy blamed by investigators for the accident.
I came across an interesting article from a 2002 issue of Geotimes discussing the various geological and geotechnical challenges of the project. Perhaps one of the more significant ones was the mitigation and monitoring of all of the existing buildings and utilities along the project corridor. Some of the buildings are historic masonry structures dating back to the early days of Boston.