These are my personal ideas, based on some rp guidelines I read so take them as you will.
Most important, establish crimes and set the timer before you search a prisoner and brig, it works out better for both the prisoner and security in my opinion.
I don’t know if this was specifically you doing this, but I saw a lot of prisoners naked and cuffed to beds within their cells. Prisoners who have not committed capital crimes should be allowed to keep their original jumpsuits in order to preserve their dignity and to save security time and hassle. Prisoners should also be uncuffed and free to move around their cells during their service time unless they have proven themselves to be a danger or nuisance.