Please use this thread going forward: Partnered Sims turn into siblings | EA Forums - 4943482
This has just happened with me as well, and I think you're on to something with the clone thing, because my sims are spellcasters and one of the them created a duplicate of herself using magic, and now when I look at her family tree...
See, the sim who created the duplicate is the one in the hat, her spouse is on her right (notice that it is now redded out), and on her left is her duplicate AND another image of her wife, BOTH labeled as sisters. They're connected to a parent that never existed, as this sim was originally generated in game. Keep in mind, I can't find any actual double of the wife any where, it just seems that the game has glitched and is now counting her twice.
I tried using MCC to delete their relationship and then restore them as spouses, but it just reverted to the having them be sisters AND spouses the next time I loaded the game. I'm seeing the suggestion to delete ALL the sim's relationships...but man, that's a pain in the you know what. Both of them have built up quite a lot of friends, enemies, and the wife has an aunt and cousin in another household. Deleting and manually restoring those would be at best a hassle, and at worst impossible.
I dunno, this is just really annoying, and I hope someone figures out a better fix before I resort to the nuclear option.
I actually edited their relationships with "remove relationship bit". I had to do this with my sims father in-law, wife, and children only. After that it said the children were her step-children and her wife was her cousin instead of sister, but the family tree was intact.
