If you make her attack you from the dialogue, you'll get a journal update saying "She attacked me and started chasing me". The same journal update should be received if you attack her outside of the dialogue.
With low speechcraft and without you being the Temple leader, there's no way to convince Calitia to surrender to House Indoril. One of the three main routes becomes literally inaccessible because of it.
It's not mentioned in Calitia's dialogue, so having this topic available from the beginning feels like some meta knowledge. Calitia should offer that as one of the solutions in "Calitia" topic.
When you escort Malkur Raran out of the troll cave, it would be nice to tell him to wait while you fight the remaining trolls. Otherwise, he runs straight to them and quickly dies.
Gebeon Estollius, the smith at Septim's Gate, has the vanilla chargen dagger you get at the start of the game in his inventory. Don't know if this causes an actual issue (since you shouldn't be able to trigger the script at this point), but worth fixing.