ᐅ Carpenter’s Error

Hello!
I have the following problem:
After our carpenter finished the roof structure, we noticed that on the visible sheathing, some of the joints are not evenly aligned, and a noticeable offset can be seen.
Also, two roof windows did not fit because the openings were smaller than required.
How can this be resolved, or what would be a reasonable solution?

You have agreed to something contractually – approach the carpenter and request corrective work.
It should be possible with the window openings, right?! The effort for the joints will probably be too high, but what does the carpenter say about that?

A correction isn't really possible since the roof is already covered. I entered the wrong batten size into the CNC machine, so the openings ended up too small. The carpenter is initially trying to blame others...