Mostly the issues are non technical and grounded in a lack of accountability and being too big to fail. A lot of these failures are failing top down. Unrealistic expectations, hand wavy leadership, and then that gets translated into action. Once these big projects get going and are burning big budgets and it's obvious that they aren't working, people get very creative at finding ways to tap into these budgets.
Here in Germany, the airport in Berlin was opened only a few years ago after being stuck in limbo a decade after it was supposed to open and the opening was cancelled only 2 weeks before it was supposed to happen. It was hilarious, they had signs all over town announcing how they were going to shut down the highway so the interior of the old airport could be transported to the new one. I kid you not. They were going to move all the check-in counters and other stuff over and then bang on it for a day or two and then open the airport. Politicians, project leadership, etc. kept insisting it was all fine right up until the moment they could not possibly ignore the fact that there was lots wrong with the airport and that it wasn't going to open. It then took a decade to fix all that. There's a railway station in Stuttgart that is at this point very late in opening. Nuclear plant projects tend to be very late and over budget too.
Government IT projects aren't that different than these. It's a very similar dynamic. Big budgets, decision making is highly political, a lack of accountability, lots of top down pretending it's going to be fine, big budgets and companies looking to tap into those, and a lot of wishful thinking. These are all common ingredients in big project failures.
The software methodology is the least of the challenges these projects face.