What a crock. Cost overruns happen on many construction project. I would guess that's true of the majority, especially large capital improvement projects. Overruns occur for a variety of reasons, including increasing costs due to economic factors (shortages of equipment, contractors and materials), delays (time is money), and market forces (more competition bids up prices), as well as mismanagement. 
There has been plenty of accountability on this project in the form of FTA audits, city audits and third-party audits (APTA). It's true they have found many problems, some of which resulted in cost increases. But follow ups have shown many of the deficiencies have been corrected. 
Fraud and malfeasance have not been cited in any audits. Rail opponents will continue to make unfounded claims and post comments full on innuendo, but so far, none have been able to show a specific case of fraud - poor judgment and bad decision making, yes, but not fraud.