3 Books Found

Based on your description:

"girl with shadow magic that she was afraid of, who was sent to some kind of school/training. There she was, trying to figure out a murder situation. Either she could see auras, or she could see fragments of the past, something that enabled her to follow people's paths hours later. She named her shadow critters something like "Beep" and "Bloop" to be less afraid of them. I distinctly remember her riding a Pegasus at one point. There was a werewolf. The school might have been a pyramid(?) She uses shadows as portals"