I've since stopped using the prisoner function for the title reason.
Whenever I use a lot of prisoners (not hundreds, maybe not even 50) the game lags and gives yellow hediff errors with things along the lines of Hediff already here/Hediff_ID not deep-saved (there are two using the same ID?). This spams the debugger and produces lag.

The mods I have that edit/create Hediffs are
Death Rattle
War Crimes Expanded 2
Life Support Continued 1.1+
and Camping Stuff