The engineering firm made a design decision to use heavier concrete construction as opposed to the usual steel frame constuction. Also, the support pilings were NOT driven down to bedrock. Both decisions were to save money at the direction of the developer.
The SF Planning Commission approved this new, different design and IMO shares the blame.
https://en.wikipedia.org/wiki/Millennium_Tower_(San_Francisco)
Transbay Transit Center developers did spend considerable money to protect nearby structures; btw there are two other new high rise buildings under construction adjacent to the site!