It's also true that those interviewing him didn't think he lied about it. Let's wait until more information comes out before we decide we know exactly what happened.
We do know exactly what happened. First, he was fired for lying, so both Trump and Pence came to that conclusion, ahead of the Mueller investigation. Then, he entered into a cooperative agreement with prosecutors. His sentencing was postponed many times, due to
joint filings by prosecutors and defense counsel. When his sentencing date finally arrived, the no-nonsense judge everyone was certain would toss the charges was actually incensed he wasn’t charged with more. Naturally, however, the twice fired, self-serving, lifelong Democrat, Flynn, just
has to have been railroaded.