The high costs of American infrastructure projects (the problem goes well beyond just transit) really stems from how we pay for them. In most other countries, there are national or regional bodies of civil engineering experts who either directly lead or heavily advise decision makers for any projects that want funding. Generally they go where the work is and can spend their whole careers gaining highly specialized experience on numerous projects. When a project is proposed they know the potential pitfalls and solutions to common problems so their estimates tend to be reasonable. If local officials come around with a ridiculous request, they tend to get shut down.

In the US management of projects is generally handled at the local level with state and federal governments only lending financial support. In any given location, any particular type of project is unlikely to be done more than once every few decades, so it is likely that none of the people involved in management have much if any experience with the specific subdisciplines a project would require, nonetheless up to date on best practices. Further, local governments simply can't afford to retain large staffs of highly specialized engineers. They may hire extremely costly consultants but there's no guarantee those consultants actually know what they are doing and their insight may be disregarded anyways. There is fairly little incentive to rein in budgets as they try to appease as many local stakeholders as possible, again none of whom are likely to recognize that their requests may be impractical. Contracts are likely to be awarded to local companies who have little experience and will need to reinvent the wheel when they inevitably face unexpected but common issues. These issues cause massive delays which are the real source of expense for most projects. Because the costs are consistently higher than expected, the higher level governments need to be willing to dispense larger grants, which in turn leads to a normalization of excessive costs.

While it is a well recognized problem, overhauling how the US finances its projects is no easy feat. For the federal government especially there are concerns about their ability to make decisions about local projects beyond offering voluntary grants, and more generally people do not like a remote government's interference in local affairs. There's also the fear that in rejecting a grant for a necessary project (even if the plan for that project is terrible) it appears to oppose the idea of fixing the underlying problem. Finally, the US gives an enormous amount of power to individuals and private organizations to legally challenge public plans which means any top down effort to impose restraint on local decision makers is basically doomed to failure.

People can call it graft or incompetence or mismanagement but this puts the blame on the specific people involved, and implies that if it were different people we would no longer have these issues. Unfortunately it is an issue with the system, which is why we see exactly the same issues across the country no matter who is in charge. We shouldn't throw our hands up in defeat, but we need to recognize the issue is real and will not be trivial to deal with.