What does that mean? That Into Darkness was bad? That Beyond was bad?
I honestly liked them both. It was a good-natured jab at Paramount, with the implication that Beyond was even more "Star Trek-y" (in my view) than Into Darkness and probably whatever was written in the original Orci script (which some report is at the bare bones for the next Star Trek film).
By "They learned their lesson" I'm actually saying "They are studio executives coming up with terrible excuses, but thankfully the best creative types behind it all know how to sneak good things behind their backs."