I have something simmilar with a Battanian Rebel clan. This is the order of events:
1. Batanians lose Marunath to the Sturgia.
2. Marunath Rebels.
3. Time passes and name changes from "Marunath's Rebels" to "Culharn's Clan"
4. I try to recruit them while they still have Marunath, in the hopes I can grab a clan to my kingdom, along with the Town.
5. Find out simply there is no option to recruit them
6. Sturgia takes Marunath from "Culharn's Clan".
7. I take Marunath from Sturgians.
8. Culharn's clan (currently at war only with Sturgians they rebelled against), declare war on Battanians.
9. Days pass, they do not join any kingdom, stay as independent clan.
10. They declare war on my kingdom (I even had a positive relation with that clan).
I can upload my savegame as well if needed.