Is there some kind of mechanism preventing the AI from accepting defeat even with a negative 100% warscore? AI Byzantium has been fighting a "lowered crown laws" war and has been sitting on 100% positive warscore for 12 years. In the meanwhile it's been devastated by invasions and lost Anatolia, Sicily and Lukania to the muslims.
Even you can't surrender if there is second war going on of your titles where the attacker is occupying your lands. So thats most likely whats happening Byz can't surrender as some areas are in control of the third party attackers who want something else from the Byz and if he could surrender to the civil war it might cause auto end to the other wars. Its there so AI or the player can't use the system to their advance by ending wars by surrendering to another that would not be that devastating than losing to outside attacker.
It could be bug only if you yourself could surrender in the same situation and only way of knowing that would be to load up as the Byzantium in the save and see if you can.