Glad they are putting it right.
In my experience dealing with builders, both at work on the design side of the construction industry & from my own build projects is that if you accept anomolies/errors from day one then that will continue for the duration of the project, as the builders know they can get away with it.
Challenging builders on their decisions & quality of work will make for a bumpier ride, but you will ultimately achieve (almost) what you want on completion.
Best of luck with your project & don’t be afraid to highlight errors (no matter how small) or question what y0u are being told – this can be stressful, but will all be forgotten once you’re sitting in your dream extension thinking how glad you are that you pushed for the correct solutions.