Windows are smaller than in the building application/work plan.

The classic also because there are always different plans and one craftsman gets version 1.0, another 2.0, and the third 2.0a. For example, in my construction, the craftsmen who poured the slab and foundation also received a plan that had already been revised several times. There were no significant changes to the trade, but now I actually have an additional drain in the kitchen under the underfloor heating. Since it does not cause any problems, it was simply left in, although it was no longer mentioned in the execution plan. As a client, you always have to check in from time to time and, yes, measure everything again, etc., especially when it comes to windows, because once they are installed and accepted, nothing can be changed. In this case, apparently no one knew which plan actually applies.

Drain and inlet water a bit wrong in the wall. Kitchen no longer fit as planned. But Ikea changed it without any problems. It's fine like this.
2. Outdoor water tap. Oh, you only ordered one? Yes, now it’s there. I ask, is it expensive? Grumble grumble... Result: it has not been paid for until today.....That’s how it is.

Every house is a prototype and not a fully planned industrial product from start to finish.

I find it already absurd to have to measure every single window as the client.

According to the building application/working plans, the windows should be 6 cm higher (larger) than they currently are. The parapet height is now also 6 cm too high.

You have to define first what you are measuring before you measure, otherwise you measure rubbish. When I read 6 cm difference between target and actual in the parapet height, I think: one person in the shell construction might understand "parapet height" as the top edge of the uppermost row of bricks, and another as the top edge of the window sill. That can already be a 4 cm difference, plus 2 cm tolerance between nominal dimension and execution. In result, I have 6 cm - 4 cm - 2 cm = 0, i.e. perhaps more talking past each other rather than actually deviating significantly.

A wrong plan version is also not "unusual," especially if the client changes something often while the first plan versions have already been distributed.

Added to that is that the important second half of document management – not only distributing but also collecting again when the release status is outdated – is often forgotten. Basically, every plan should say: "If older than 14 days, then actively ask for validity confirmation before execution."

It is enough for you to have one black sheep among your trades to spoil your fun with the house for a long time and cost you a lot of, lot of money.

And exactly this risk you increase quite reliably if you look for salvation (squeezing out the last cent) in individual contracts. Many more houses could be free of defects that cannot be overlooked if not so many homebuilders would bother to deliberately bring a rotten apple into an established team.

I was at the construction site at least twice a day. In the morning before work and sometime in the evening when no one was there.

I have not re-measured the windows to this day. They are fine with me. What is in the plan does not matter to me. If something is important to me, I take care of it during construction. If I don’t notice that something doesn’t fit, referring to the appearance, it can’t be that bad.

People work on construction sites. People make mistakes. Anything can happen. I think our general contractor and the craftsmen did a good job.

Rectification of defects must always be proportionate. Replacing a window because of 6cm is probably not.