I was in the sales area, buying cheap horses in order to FR them to complete a quest. I'd buy 10-20 at a time, close the tab with the horse, then go to my Incoming #1 barn to mass FR them (which has worked multiple times in the past) -- only the barn was empty each time. I know I'd bought them, because I received the "Congratulations" message at the top of each horse's page.
So I started buying two or three, closing the tab without FR'ing them, then opening the barn (by clicking on the location in the horse's bio) to see if they were there. They were, so I kept on buying.
As I was buying, the popup appeared indicating that I'd completed a HE quest -- and Incoming #1 was completely empty. In the place of the FR quest was the quest to breed a Premium Brindle Foal.
This problem only happened with purchased horses -- the foals I bred this morning were all in Incoming #1 (which isn't my original barn, but a barn I purchased well over a year ago), though I moved them to another Incoming barn to make room for the purchases, so I could mass release the new horses instead of using the dropdown, which can be incredibly tedious when you're using it on hundreds of horses.
Something is up, and it isn't good. I'm afraid to go over and look for new breeding stock in case they might be FR'd automatically as soon as I buy them.