I have no doubt prison has these sorts of effects but I have a strong sense the reported effects are exaggerated. What do you think about the design of the analysis (click through the link in the NPR piece to the journal article - there's info to glean even fom the abstract).
I've spent a lot of time in the NLSY. There are about 9,000 youth in it, so when they refer to "tens of thousands" I think they mean across multiple waves. Only a small portion of these youth are ever incarcerated - it was so small that my co-author and I couldn't do much with it when we were looking at employment rates for young adults. So that's an issue, but what else concerns you here?
UPDATE: I should add - the author may very well have listed all these limitations in his article. That's not unusual at all and in my mind it's perfectly appropriate: dig up what you can and qualify the hell out of it. But this NPR report does not seem to have the same caution.
2011 And All That
48 minutes ago