Wynand made the following booking LHR-WAW-BUD-ZRH-IST-ZRH (-?!) and was advised that transiting ZRH twice would make the IST section count as a side-trip.

You have a side trip ZRH-IST-ZRH (=2nd ticket), because ZRH appears on your homebound itinerary twice and not because you are transiting in ZRH twice! Your final destination is WAW (= point of return), which does not count as stopover. Subsequently you are travelling back to BUD and ZRH and forward to IST again.