This is how FamilyEcho handles this situation. Juan is not the father, Marigold is his wife's daughter.
To create this:
Act faster than in real life 
- Give Stephanie a husband, Victor. Set their partner-type to divorced.
Create the child Marigold, you will see the correct partner will be suggested.
Give Stephanie a new (primary) partner, Juan. Set their partner-type to married.
Presto.
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After Dantes reply I added this:
When I click on Juan everyone appears just once.
So yes, I did not really react on your main complaint. The reason is simply that I think that I can show that what you encountered is not the normal working of FamilyEcho (and did so?).
But please: clarify how I could have told you what you really wanted to know, I must have misunderstood you, sorry. (I am just another end-user, reacting to help out, if possible).
This is where and how duplicates are functional (example):
Jan Koning, below, has both grandparents from his mother's side and grandparents from his father's side.
His wife Guurtje Noome, next to him, has both grandparents from her mother's side and grandparents from her father's side. The thing is, they are cousins AND they married.
So their children could have had eight great-grandparents, but now they have only six! (the ones in this answer in bold italic text, Jan Noome sr and Trijntje Laan being the same people on both sides).
FamilyEcho depicts all eight, if only because now you see exactly who the parents of Jan Noome jr and Neeltje Noome are.
But they are annotated on one side as being Duplicates.
This could have been drawn differently if it is the only anomaly, but before you know it things get too complicated.
So I can surely live with their solution. Elegant enough, it is, even.
