go to your deployment, is your prison blinking yellow?
The prisoners should be able to leave their cells to go to certain rooms such as the yard and to get food etc...
Usually it won't class your prisoners as uncuffed in case they believe there is something wrong with the prison.
My thoughts also come down to the cells needing to be connected to a hallway which attaches to each other room/building as they need to have certain paths allocated to staff/prisoners/High Warning Prisoners.
Look at what areas are marked as. i had this problem because one of my main hallways was marked Medium only so my high risk guys would do nothing else. had to switch back to shared. worked fine after that.
There you can see paths connected to each cell and the locations they can go to.