Hi Alexey,
Thank you for your response. There are coordinates assigned to the photos since they were taken by a drone. The markers do not have coordinates assigned to them. I have something processing right now, but I will check the coordinate systems in the Reference pane soon.
I processed photos from a previous drone survey this summer, same parameters, and had no issues like this. For the survey this summer, there were ~300 photos and 6 markers, and for this survey we have ~500 photos and 11 markers. Would either of those things affect it?