That's very strange, do you happen to have a save from just before it happened?
This is...weird. I did not have a save from before it happened, but i loaded my game as the messed up Tully's so i could screenshoot the thing and it was...fixed? I mean, not really fixed, but changed around. Now my "adopted" Tully and descendents were correctly displayed in the family tree. But the old Tully's, the "real" Tully's are now where mine used to be, featured in a single column to the side of the tree.
Like so:http://cloud-2.steampowered.com/ugc/577864117840931080/FE956FC89DF417886D9838BA245820F1F2DC092B/
But to be clear, is this not meant to happen during a game? Because the broken family tree happens anytime I design a ruler and make him a part of an existing Westerosi house. But is there an event somewhere that mimics this? I tried to find it but failed.