Numerous other buildings in SF have moved around after being built.

Unlike most of the other buildings using the foundation system that's described in the article, the Millennium Tower is all-concrete. One does wonder if the greater weight of that type of construction, when used with a "traditional" foundation system more typical of steel buildings, might contribute? That said, the engineers signed off, and the City signed off, so "not meeting code" isn't a valid excuse at least at first glance.

The article looks to me like a first salvo in the process of deflecting lawsuits over settlement of the building to the Transbay Transit Center project. It wouldn't be the first time that underground work and deep excavation in SF's fill areas caused some movement of surrounding buildings. The Transit Center project allegedly was designed to avoid or minimize that, but somethings things just happen in the downtown muddy goo. Given that the Transit Center's a publicly funded project (i.e. Deep Pocket), I expect that We will eventually pay for whatever fixes are needed, whether or not actually related to the Center construction, in order to avoid a long court battle.

FWIW, not all big buildings in the area use load-bearing piles into the firm sand layer. The Embarcadero Center complex was noted in the engineering and architecture literature at the time it was built for using a system similar to what's used in Mexico City: the complex essentially floats in the mud, with pilings driven to the sand layer as anchors rather than support. IIRC the BART stations in lower Market Street are similar - they have pilings, but mainly they're floating as submarines in the mud with a lot of ballast to hold them down.