With Safa's god eyes, there were a few things that she was able to see: the large flow of mana in the room, the flow of mana around certain individuals and devices, and in particular, what type of mana was being used.
All of the vials that the religious members were taking, including the energy and powers they were using to attack them—all of it was light magic. It was why her Lux sword was acting up as she entered certain places and why she was able to even counter and control other magics that were being used her way.
The round sphere-like device in Carl's hand, she also knew that it was a device that was powered by powerful light magic. Knowing a few light spells herself, she had assumed that the flash of light was to blind one's opponents and then give them the chance to attack.