You can see it says the Prison holds 6 prisoners, but there are 7 units inside. I have a hutch it happened because I saved at the moment it was being dragged inside, because I just defeated the group pictured and they were en route to the Prison when I saved.
Although his issue is correct, the issue has nothing to do with savefiles. I have recognized this bug multiple times. It seems an enemy can "get stuck inside" right after you take over a prison. The enemy then isn't flagged as a prisoner, and as such it can also not be picked up, but you can however lightning bolt it. (Something you cannot do with normal prisoners)
Interesting I'll make a note to investigate this further in the coming weeks.
I've simply not been able to figure this out after several hours of testing today. Tried both save and load testing along with large scale prison capture testing. Unfortunately nothing seems to yield results. Overall this is a fairly minor issue so I'm going to close it down as unable to replicate but if more info ever comes to l ight let me know :)
Please upload your savefile for this level, thank you.