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It's an inherently hard project that's costing way too much.

The East Side Access involves building another level of station underneath Grand Central Station, without disrupting service. The tracks are 150 feet below Park Avenue. They're working around skyscraper foundations, and adding supports for buildings above. Look at some of the pictures on line.

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The article goes into this though, these challenges are something that comparable international projects have faced in much worse ground conditions (which extenuates the issue).

The magnitude of cost difference does not stem from engineering challenges.

Exactly. Crossrail in London had some insanely difficult challenges (like threading a new subway tunnel between two existing ones with only a few cm of distance between them), and hitting an enormous ancient Roman burial ground at Liverpool Street.

Despite that (and many more) it is currently 6 months ahead of schedule.

There's a great documentary about the project called the fifteen billion pound railway which covers a lot of these challenges.

Don't forget that they did that bit of the tunnelling on a Monday morning, there were some tense looking staff on the platform that morning :)

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