After another hour(I lose time too easily, probably much more) I think I know the reason for this strange behavior of the cursor.
So I think it was the fault of the lack of resolution in the settings for my monitor.
It's just either smaller or larger.
Setting any resolution higher than that of my monitor does not immediately cause any undesirable effect.
However, when some function under the hood refreshes the screen size it causes the game screen to change size rendering part of the screen off my screen.
In case of not too high resolution (1920x1080) it may not even be noticeable.
From here I think there is a bug with the cursor because the game thinks the window rendering space is larger than the mouse cursor coordinates space.
Which causes the cursor to be mapped to a different part of the screen than the graphical representation would indicate.
The solution I used:
I added my screen resolution to the config peak and set it to read-only (I didn't check if it was reset but I didn't want to play with testing).
Setting a lower resolution available(1360x768) was not an option for me as the game becomes annoyingly blurry .