This is a challenging situation that many among us have encountered. There is no easy way around it in a data structure that connects each person to no more than one father and one mother, and does not provide for fuzzy connections. Maybe someone will devise a new kind of structure that allows family trees to skip across a parent generation to get from a child to a known grandparent.
In WikiTree you can use the text section of the profile to discuss the situation, and link to the profiles of identified relatives who cannot be connected as immediate family.