To be honest, once your prison is large enough and you have hundreds of prisoners of all types and security levels, the programs tab is such a chaotic, unmanageable mess that I almost gave up on managing them as I'd like to, and I just spam "start" until I get the error message, and then I know I don't have room for more of that type... so I hadn't noticed this bug affecting all programs.
Have the devs said anything about this? AFAIK it hasn't been adressed in The Pen, so I guess we'll have to wait until the next paid dlc comes out.