I’m going to be a bit controversial and go out on a limb and say nope to this T......the builder appears at fault....works not in accordance with the contract should be ripped out and made good at no cost to the client.....and any delay to any timescale project is his responsibility and his alone - and he should know this.
Foundations are notorious difficult to determine before works start and should be remeasurable based on rates - whether from a spreadsheet of from agreed rates.
Yes - the architect and engineer may ask for additional fees but I’d like to think that any professional worth his salt would be embarrassed to ask for much if he delays in getting the information to the client in a timely manner. There’s no excuse in this day and age for an underpinning detail to take several weeks to deliver.......
For what it’s worth - and if you are happy to accept any the mistakes he has made continue. If not move on but be wary of any contractual conditions in relation to contract determination.