i have the same problem. a same-sex married couple suddenly became brothers — i suspect it happened after having their second science baby, everything was fine for a long time.
the worst part is that there’s no way to fix it — i tried removing their siblings status via mccc and via ui cheats extension, after anything that involves a loading screen they become brothers again. their relationships cannot be changed in cas. i tried saving the family to gallery, deleting one of these sims in game and adding him back — everything’s fine, not brothers, then i used mccc to again make him a husband (still fine), then reloaded the game — right after that they’re brothers again.
i gave up and unfortunately had to get a mod to force the game to ignore that they’re siblings to continue playing since it’s my main family in my main save.
upd: okay i got curious and decided to experiment a bit with it, so i saved my family to the gallery and started a new save only with mccc. i tried both adding them as one family straight from the gallery on world map and adding them by entering cas, choosing the family in the gallery and saving — the game showed them as husbands and brothers at the same time in both cases. so, i tried adding each of my sims separately in different households so there were no connections between them, then i joined the households and got them married (at this point not brothers, only husbands), saved the game and entered cas with cas.fulleditmode, then left it using X, not checkmark button — boom, they’re husbands and brothers. then i loaded the save i’d made before entering cas — they’re already marked as brothers. so for me any loading screen would result in changes in their relationships. i removed the siblings relationships between them in mccc and tried adding different parents to each of them in cas — the game wouldn’t let me add parents to one of them as if he already had parents, like it wasn’t even an option is cas, so for him i just created two sims and assigned them as parents using mccc. after that, when both of them had a separate set of parents, they wouldn’t get marked as brothers no matter what — leaving cas using X, using checkmark button, reloading, adding a science baby — everything’s fine. as soon as i removed one set of parents they got marked as brothers again, but the remaining set of parents doesn’t see the orphaned sim as their son.
so, basically, the only way i’ve found to avoid this bug is to manually remove the siblings statuses and manually assign two parents to each of them using mccc, because the game itself doesn’t let you do this, and keep these parents in the game.
(another curious thing i’ve noticed during this — if i remove their siblings statuses and enter cas, i cannot create a child for both of them using genetics, the game doesn’t allow selecting the second sim as another parent, so they in fact get marked as brothers again during loading, not after leaving cas, although in cas the game shows they’re first of all spouses, not siblings)