Given no choice after conquering a city

I notice in some rare case, after I conquer a city, I didn't get any choice - the city is automatically annexed. For example, in my current game I just took Edirne from the Ottomans, and it didn't give me any choice to puppet or raze it. Edirne isn't the Ottomans' original or current capital, and even if it were, puppeting should always be possible, right?

Is there any condition that would trigger such treatment? For my future reference.

That sounds like the auto-annex bug from vanilla that would sometimes occur if you conquered a city that used to belong to a third party.
I'm not sure if the fix for it in G&K was ever "back ported" to Vanilla.