Error in the countertop, allegedly natural…

I would first check whether this is really a natural inclusion or if cheating was involved. This can be done with heat. Natural stone is heat-resistant, quartz composite is not. So put a nice roasting pan in the oven at 200°C (preferably put a duck or goose in there beforehand, so that the energy consumption is worth it, and when finished, place it exactly there. If the stain is still exactly the same as before, then it is probably really natural. If the stain is discolored, it is a repair spot and clearly not a natural inclusion. Then I would also complain. I don't know if there are less invasive tests because normally a "destruction" of the countertop would hinder a complaint, but in this case the manufacturer would be caught.

Here the stonemasonry company simply did poor work. Professionals would have noticed that and would not have processed it that way. With leather, insect bites are also taken into account and the spots are processed in inconspicuous places. The carpenter also ensures that there is no knot hole in the middle of a homogeneous wooden tabletop. Of course, nature should look natural but not like this. Another good example is dead pixels on a display. Up to a certain number, one has to (or had to) accept it. But I could not constantly look at a display with a dead pixel. That makes my inner Monk go crazy.

I would first check whether this is really a natural inclusion or if there has been some cheating here.

It can quite possibly also be a natural cavity that was perhaps filled completely correctly, as provided by the a.a.R.d.T. Cheating is therefore not necessarily the case, and discoloration is no proof that it is a natural defect.

Above all, white putty should not have been used, which would have been immediately complained about by the customer. :rolleyes: The OP should look through their contract documents to see what is stated there about deviations and the chosen stone quality class. Everything is defined.

Already during the assembly of the kitchen, we noticed an inclusion (about the size of a 20 cent coin).

Not only do I find the size estimation exaggerated, but I also do not consider it to be an inclusion (which indeed would not be a "defect" in a natural product), but rather a sloppy spot repair attempt.

In the picture, it is not possible to tell whether it is nature or a repair? If it is a repair, then definitely complain. A better photo could help.