Strange diplomacy

In a pontic campaign I sent an army to take Nikaia. Just before the city an Eleutheroi army from Pergamom attaked me and killed my faction leader, but I won the battle. When the AI turn ended all my allies broke their alliances with me. There was no message warning me that taking Nikaia would cause war. What happened?

Perhaps you didn't have the script running when moving into the area? Or possibly you'd got the warning sometime earlier in your campaign. Possibly it doesn't detect as well when unloading from a boat too, I don't know. It is correct that taking Nikaia causes consequences.