Most big projects of this nature come in over budget. The reason is the incentives of the politicians coming up with budget estimates.
If they come up with a realistic (high) estimate, the project doesn't get done. That's a political loss - their cronies don't get paid, and they don't get to put their name on a big project. If they come up with an unrealistically low estimate, their cronies get paid and they rarely get voted out of office.
Last time London hosted the Olympics was post-war 1948, on a budget of less than a million pounds (I'm not sure if that figure is adjusted for modern currency or not, but either way it's not much money) - they didn't even build any new buildings for it.
The first, a combination of incompetence (e.g. forgetting they'd have to pay VAT) and corruption. The latter: by getting into debt, that now necessitates cuts to the very things being celebrated, e.g. the NHS.
We spend more on interest on government debt in the UK than we do on defence.
This being the 3rd Olympic event in London, I'm surprised the estimate was that much off.