Thanks for fast response.
I did what you suggested and it zooms out to show only the area I want, but I think I've found what caused the issue.
I've tried to erase consecutively all tools and deleting all windows from the plan, made zooming to extents work properly. I looked deeper in the window options and when I turn off window marker "Aus Win & Door Marker 20" everything works how it should. It seems that the glitch was caused by marker's "Text Wrap Frame" parameter, which shows as three hotspots - a center one and two side ones. In some instances only a central hotspot was visible, so I assume this was the reason for this unwanted behavior.