Actually, teams rarely "figure out" opponent game plans without enhanced scouting techniques, although the best do a good job of seeing substantial trends and predicting particular plays of their opponents, to their benefit, without them. No scout or coach is as prescient and/or precognitive as those with a video tape or digital recording of the actual signals and plays...
Also, not all teams are the Patriots, and not all coaches are Bill Belichick. As the article noted, and as I noted above, the league had a huge amount of tapes proving Belichick had flagrantly and systematically taped numerous teams' signals and plays. And it was also clear Goodell quashed any substantial investigation and penalty of that taping, which emboldened Belichick to do it further.
So, since it was also apparent Belichick had taped the Rams (as well as many other teams), it was highly likely Belichick would do so against the Panthers and the Eagles, particularly since he knew Goodell wouldn't punish him and risk bad publicity. And of course it's "easily conceivable" the Eagles just screwed up. It's also easily conceivable Belichick taped their plays--including that "rarely used" scheme--and used that taping to help himself and the Patriots beat the Eagles in the Super Bowl. The same goes with Henning and the Panthers.