In my game the rowing clans were close to economic victory so I decided to wipe them out. All of their heroes died, all of their cities have fallen, but a few sea fortresses remained  so they were still alive . They still had a few small armies and fleets with absolutely no way to generate income (actually because of the remaining forces their income should have been negative). I've been chasing their forces for a while (they were always retreating never fighting...) but simply couldn't get rid of them all. Once I thought that they have all been finished then a new unit appears somewhere from the FoW.

The problem was that even though they were pretty much wiped out, they STILL MANAGED TO WIN the game by acquiring some more money (I have no idea how).  I've tried loading a previous save, asked for money for peace (they had only 15303 dust I could ask for) I got it YET they still managed to get that amount without cities.  

Why is the enemy still alive if he does not have any cities? If they only have fortresses they might have some remaining fleets, but they simply not able to win the game from that state. 

Also, he has lost everything, yet signing a truce was extremely expensive I had to handle over a few technologies. How does that even make sense?

Additional notes: 

The enemy attacks an empty fort I have reinforcement fleets around, I beat him, win the battle YET HE STILL CAPTURES THE FORT. 

If I'm garrisoning the fort, the enemy attacks with 2 fleets but does not bring in the reinforcement fleet, and I defeat the primary fleet, I still LOSE the fort and my fleet appears outside of it.

But if I choose not to use my reinforcements, the battle still plays without any forces of my own.