Hi Maciej,
Thank you for your question, and welcome to Archicad!
As runxel mentioned, this is indeed a limitation with the current method of intersection in Archicad (before Archicad 17). We can always switch back to the old intersection method by going to Options > Project Preferences > Legacy, tick the checkbox
"Use legacy intersection..."
, but I would not recommend this, as it may bring some potential issues when the project grows.
I entered it as a wish in our Wish List database to improve the current intersection method (please refer to it as #12899). Hopefully, our Product Management team will adopt this one in the future!
Thank you very much for your understanding. Have a great day!
Best regards,
Minh
Minh Nguyen
Technical Support Engineer
GRAPHISOFT