I'd like to load up your save and help confirm, but alas I'm still playing the demo version of the game.
I also noticed this behaviour in the demo - signed peace treaty with Elizabeth, which expired, then she declares war on my city state ally and I can't assist because the Declare War option is greyed out.
Could it have something to do with the city state diplomacy mechanics? Eg, you accept a new city state ally who is at forced peace with the opponent, and you must wait for that deal to expire?