A couple points, that helps give a clearer picture;
1) The original budget by the City was clearly not enough to do the job, so reporting these as "cost overruns" is a little misleading, as it implies that money is being wasted, instead of not enough money budgeted to begin with. The sheer number of unforeseen conditions on this type of project all but guaranteed that. Everyone knows that when you bid/budget a shop off nothing but vague architecturals, with no detailed design, the price needs to be much higher to account for the significant risk or those exact conditions. Clearly, this did not happen.
2) In the midst of construction, Vanbots, who had just been recently acquired by Carillion, went through a massive change in personnel during the period of 2010 - 2011. Lots of old Vanbots personnel left for other companies, and green staff thrown into the midst of Union Station. This had significant impact during that time period, and was completely outside of City control.