Another weird bug to point out: Somehow my prison and secondary prison in construction suddenly became Cryo-prisons, much to my amusement, with the increased capacity they bring, although I couldn't check the prisoners' pool, bringing me to the sell menu as mentioned before. Their ufopaedia entry remains the same as well.
Building another prison seems to work though.
Yeah, the CryoPrison upgrade when upgrading mid campaign is a bit of a surprise or easter egg. The issue is that the old prison used the STR_ALIEN_CONTAINMENT from vanilla, and 99i1 is using this for the Cryo Prison.
If you don't want to feel like you are cheating, you can edit your save and replace the shiny new Cryo Prisons with the new Jails. Find and replace the - type: STR_ALIEN_CONTAINMENT facilities with - type: STR_JAIL in your .sav. this is the approach I took.
Also, the Cryo prison will get a fix applied in the next version, by allowing prisoner management with the right click instead of opening the fence menu. To manually fix this, Open piratez.rul. Add
rightClickActionType: 1
To the - type: STR_ALIEN_CONTAINMENT entry.