Unfortunately cost overruns have been a feature of major railway (and other) construction since their birth. Generally, the smaller the project, the less risk of overrun.
You get a contractor in to replace your kitchen - gives you a price (but its very low profit margin as he wants to win the contract and price is the main factor), you can just afford it, give go ahead. usually works out ok. Now suppose that plasterboard wall you wanted knocking down to open up the kitchen turns out to have a solid brick supporting wall hidden behind it? It was unforeseen, but you only had what you accepted in quote, the contractor hasn't allowed to be on site for longer and wants to go to next job or leave as on temporary contract. So, you have to borrow some money, the contractor has to suggest a price to fix the problem (they often DON'T fully cost the remedial works and give off the cuff figures which are too low and cut into their margins and the work takes longer. Whenever I have encountered cost overruns on projects of whatever type, the 'extra' is NEVER the full amount of what the extra work costs - which is why cutting the initial cost to the bone to win the contract can be a pyrrhic vistory.
Now that can easily happen in your kitchen, try multiplying that up by hundreds of thousands.
The estimated cost of a project is just that - it is NOT the cost, its the estimated cost. When you give the customer the projected cost, the usual response is I never thought it would be THAT much. They then start a process of knocking out certain features they don't deem critical to get to the price - what can possibly go wrong? Well, if you were to have a project with 10 major elements, and you removed the estimated cost of 6 of them, the remaining parts would likely cost a lot more than originally envisaged because you haven't got the base core which was necessary and whose cost was shared between the various sub parts. This is often given cursory attention by Project Managers as they feel they've nearly got that vital contract and can absorb or maybe charge the extra costs, but they haven't properly reassessed them which they should..