It appears the problem occurred when the project design firm, hired by DelDOT, missed the duct. They would be the ones as fault.
DelDOT can go after that firm for the money. At the same time, the firm is going to say that DelDOT also should have had knowledge of the duct being that they also had the blueprints, reviewed the plans and were ok with everything.
Here's a slightly more indepth article from the (Wilmington, DE) News Journal:
https://www.delawareonline.com/story/news/2018/02/19/del-141-bridge-mess-continue-into-march-cost-taxpayers-least-extra-million/351231002/The article notes that DelDOT can submit a claim to get the money back. Doing so though will probably cost DelDOT a firm they've done a lot of work with in the past. Being that, according to the article, the project was greatly under-estimated in cost and time, there's plenty of blame to go around.
The taxpayers will probably be eating the cost on this one...because most likely even if the duct was included in the demo plans, the million dollars would've been added onto the original bids anyway.