The text of Proposition 1A that California voters approved in November 2008 (before Obama took office) estimated a cost for the whole system of $45 billion (
https://lao.ca.gov/ballot/2008/1a_11_2008.aspx). The 2024 business plan has a Phase I (S.F. to L.A.) cost of $89–128 billion. You can cherry pick the $128 billion number, but it is meant to include quite a large contingency for unexpected costs. Nonetheless, the actual costs are clearly higher than estimated. As I understand things, there are a few big reasons:
(1) Much higher construction cost inflation than forecast, both because we've had more inflation than expected (particularly between 2020 and the present, and particularly in construction) and because construction has been much slower than forecast because the private and federal funding the state was hoping for didn't come in the amounts hoped for. Based upon the data at
https://edzarenski.com/2024/01/17/construction-inflation-2024/, "non-building infrastructure" inflation has been about 65% since 2008. Highway cost inflation has been 100% since 2008.
(2) There was money wasted early on because the conditions of federal grants pushed the state to start work before it was really prepared. Eminent domain and utility issues slowed down construction work and drove up costs. Not good, but not a primary driver of the topline cost increase.
(3) What is actually getting built is bigger in scope than what the estimates were based upon, in terms of aerial structures, grade separations, freight facility relocations, noise mitigations, and the like because BNSF, UP, and cities along the route (or combinations of these: city demands route than crosses freight route, and freight railroad demands that there be zero—or beneficial—impact on its operations) demanded these expensive changes, and the HSR Authority didn't or couldn't push back.
There is also no doubt a lot of money that could have been saved if the state hadn't been so reliant on outside private consultants, who are expensive and don't really have strong incentives to control costs. There are also probably excessively generous deals with unions and excessive insistence on Buy America rules.
But I think the real failure here is not incompetence by the folks at the Authority or their consultants. For them to have succeeded, they needed a predictable and realistic funding source and political backing that enabled it to say no sometimes to the demands of local governments and the freight railroads. Instead, we've had a state government unwilling to kill the project but only willing to give it the minimum funding to keep it alive and an Authority that politically can't afford to make enemies, even if that's what it needs to be willing to do to control costs.