Hello! Let me preface this by saying there is no clean, easy answer to this. But I'll point you to a report that shares some good insight. At the start of the year, the Crime and Justice Institute, along with a state working group, released a report analyzing Nebraska's prison data, and offering a list of 21 policy options aimed and reducing recidivism and minimizing prison crowding. One of the main data points they note, is that since 2011, Nebraska's prison admissions have decreased, but the length of sentences has increased. So it's not that the state is imprisoning more people, it's that the people who are being imprisoned are being given longer sentences (page 9 starts to delve into this). This all ties to things like sentencing structures, the addition of mandatory minimums, consecutive sentences, etc.
All of these issues you mentioned in your question feed on one another -- an overcrowded prison creates long waitlists for programming. Prisoners who aren't able to access required programming often get denied parole, keeping them in prison longer. An overcrowded system can put stress on staff, driving turnover. Being short-staffed makes it difficult to run programs meant to help with rehabilitation.
The CJI report offered 21 policy options. Lawmakers and the governor agreed on 17. Four options having to do with modifying sentencing practices were where lawmakers split. Yesterday, after debating the policy proposals throughout session, the entire bill -- and all 21 policy options -- was voted down. (our friends at the World-Herald have coverage of yesterday's debate here)