I suspect much of the problem is that Millenium towers is built over was once water. There is a deep layer of old mud, and supposedly bedrock under the old mud. What is bedrock, that has been under water for millions of years? Probably nothing like granite or dry rock.

The Salesforce tower is just west of the Millenium tower, and it is much larger. It was built over originally dry land, and is not sinking.

The map below shows the original SF waterfront, and where old ships were abandoned next to piers. Seaman left for the gold fields and the ships rotted away until they could not be sailed.

This is a pretty well done comprehensive video, released on the 1 year anniversary.