NYT has a great writeup on the East Side Access tunnel. In short, the costs work out to 3.5bn/mile (!), there's ~200 "ghost" workers, and the usual spot of corruption and favoritism. It's a mess, and the MTA is deferring regular maintenance to pay for it. https://www.nytimes.com/2017/12/28/nyregion/new-york-subway-...
200 ghost workers at $100K per year (probably a bit high, thanks) is $20 million per year.
Um, so much for that causing the cost overrun.
Project management is generally the failure. And, generally, it starts with the asinine "low bid" rules.
Everyone successful at dealing with the government knows that you bid as low as possible to get the contract and then you charge them a fortune on the back end.
Edit: Okay, even if I BELIEVE the $1,000 per day (and I don't) that's $300K per year and is still only $60 million.
Edit2: I have read and searched the original article several times and cannot find that $1,000 number anywhere.
Edit3: Oh, it's in an article linked in the comment. And the linked article says that they laid off those contractors once they found them. Project management and oversight failure--again.