I'm going to try and explain this as best I can without outing myself totally.
We are having a huge renovation at home, we had several quotes from builders and chose one we were happy with. The quote was based on all the relevant drawings and planning permissions which were submitted and agreed BEFORE we got builders quotes.
We are now mid way and the main bulk of the work is underway. We have had an issue which was part of the original plans but has had to be changed because our builder couldn't do it the way that was needed. this has incurred additional costs which our builder has asked us to cover.
Our builder has been great so far and we are happy with the work however we have a tight budget and were not expecting this additional cost which is no way our fault - we have not changed any of the plans etc.
I don't want to piss our builder off as our house is currently half built.
Why can't he do it the way that was needed? If the change is to suit him, he pays. If the change is because your plans were untenable, you pay. That would be my assessment, but I know nothing about it.
It's usually advised with large renovations to leave some money aside for unexpected problems along the way and also to expect to go over a projected deadline for completion.
Not sure of the money involved or the obstacle your builder has encountered however so it is hard to comment. Could you get a second opinion or go back and consult the original planners that drew up your plans?