It seems you (and/or your company) have a fundamental misunderstanding of what a family tree is supposed to be.
Let me clarify, I also work for a company that has (as one of its products) a family tree in its portfolio, and we have been struggling with similar problems.
The problem, in our case, and I assume your case as well, comes from the GEDCOM format that is extremely opinionated about what a family should be. However this format contains some severe misconceptions about what a family tree really looks like.
GEDCOM has many issues, such as incompatibility with same sex relations, incest, etc… Which in real life happens more often than you’d imagine (especially when going back in time to the 1700-1800).
We have modeled our family tree to what happens in the real world: Events (for example, births, weddings, engagement, unions, deaths, adoptions, etc.). We do not put any restrictions on these, except for logically impossible ones (for example, one can’t be one’s own parent, relations need two individuals, etc…)
The lack of validations gives us a more “real world”, simpler and more flexible solution.
As for this specific case, I would suggest removing the assertions as they do not hold universally.
For displaying issues (that will arise) I would suggest drawing the same node as many times as needed, hinting at the duplication by lighting up all the copies on selecting one of them.