Sorry to hear about your troubles Tom. Having been in construction for 32 years and a general contractor for the last 26 years I have been on both sides of the table.
I have had subcontractors do the same thing and it is always a difficult situation. On one hand you have negotiated a fixed price with the client and on the other had the mistake not occurred the cost would have been included. If it was a small amount I would work it out between myself and the subcontractor and not involve the client. If not then I would negotiate with the sub and client to come to a compromise. In those cases nobody wins with the subcontractor loosing most if not all of their profit, my profit is reduced due to the subs fault and the client is less than happy.
As for deadlines that's a tough one. Sometimes you're a hero sometimes a zero. We loose sight of the fact that homes are built by hand by people of all different backgrounds, skills, and ethics. Construction has a lot of moving parts with people, suppliers, manufacturers and good old mother nature which can be difficult for even the best of construction professionals to keep a handle on. I refer to it as adult day care.
I'm not trying to take the side of the contractor since I know nothing about them, only trying to point out it is a complex process and some people do it better than others. I now do construction consulting for construction defect litigation and I have seen the worst of the worst. In the past I have taken over several problem projects that were behind schedule and over budget and most of the time it was due to poor communication and/or business skills of the contractor. Unfortunately it is too easy to become a contractor. Other times the client was just batsh*t crazy. Nothing like walking into a situation where everyone is p*ssed off.
Unfortunately right now the contractor has the advantage knowing you need this to be done as soon as possible. Hopefully you have a retention at the end of the job you can use as leverage to negotiate the final payment since it will be a portion of the contractors profit and the ball will be in your court. When things start going south I keep a log of all the conversations, promises, dates etc. that they occurred That can help at the end when memories get cloudy.
Hopefully your new home will be done soon and this will all be a distant memory.