There are quite a few bugs in the story that involve getting into combat with a monster that was introduced in a previous step that cause the story to stop progressing.
One example being killing the security golems in Rata Novus after you’ve activated the ley line consoles and started following Taimi.
Another example is in the mission where you activate the ley line map when you fight through a few mordrem to get to Taimi. Once you’ve activated the map and, if there are still mordrem guards from the triggered traps in the previous step and you attack them, the story will cease to progress.
I believe a similar issue happens when I suddenly enter combat on the story mission, “Sign Cutting” while simultaneously discovering one of Rox’s trail markers.