Hi.   During the mission, right after reaching Palatine,     most of my actions like visiting the church or laying down the ambush is impossible.  I tried visiting the princess and it worked at first but  once I left, i couldn't come back inside the prison. It all started because I didn't have access to the city by the time I was progressing during the mission but the mission kept going anyway.

For some reason, talking to one of the guild leaders and closing the conversation allowed me to go to the church and the prison but I still can't lay the ambush.

Btw, Lyra is a NG+ character, maybe I got her mission much earlier than anticipated.

Here's the save file

Happened to me, too. The 'use the caravan as bait' option worked for me after I went back to an earlier save, but the 'nice' way seems bugged to the point of broken.

Also, there was a bug after the mission that just repeated the first scene when you get her. 

Having the same issue. I unlocked Lira through the story and have already done the other quests, so I was confused as well as to why some options simply didn't work.  I thought "I'll just exit and reload the save", but this completely resets Lira's quest.