It's just an alternative truth.
There are no alternative truths, but there are alternative scenarios.
Somehow, Flynn made it all the way to Lieutenant General, so he must have something on the ball. Lying to a superior officer is not the sort of mistake one would expect from such an experienced player. So, what happened?
Suppose it worked this way: Pence was in on the phone calls and knew the details. He and Flynn determined the incident was deniable, so Pence goes out an makes a definitive statement of fact, giving full confidence to Flynn. Shortly, leaked information reveals that Pence's confidence was misplaced.
One thing which has always held true about Inside DC Politics: when a leak results in a high level person losing their job, the leak is most likely an inside job and the sole purpose was to throw someone under the bus.
In the cold light of day, Flynn was fired for embarrassing the Vice President, but the VP didn't have to make the statement. They could have stonewalled and nothing would have happened. There would be a lot of noise from the Democrats and the press, but they'll always have that. The real question becomes, was it Bannon or Pence who wanted Flynn off the team, or was it both?