Might be where the conflict has it's roots, who knows.
Put yourself in Pep's shoes and suddenly you see dilemmas all over the place:
Lowering the intensity in training preserves health, on the other hand it's a basic requirement to internalize playing sequences in an intense playstyle. And it's required to somehow keep a healthy level of stress in the team, especially when Bayern seemingly is about to win the league in late November, metaphorically speaking.
Then you have players who are essential to what the coach wants the team to play. Fielding these players though every match might guarentee short term success, but the injury risk is unproportionally increased. Yet not fielding them or resting them might get them out of playing rhythm and leads to them falling into discontent with the man management. Coupled with the fact that one of these essential players, Robben, is known to be a glass cannon.
The same goes basically for the general tactical setup, it requires permanent compromise between what the coach knows works, and player fatigue and injury risk. And as a consequence, the question arises whether the coach should abandon a tactical setup he knows is perfect because it might be too physically draining for the players. Extreme example here is Bielsa, who basically leads players far beyond their physical possibilities with the idea in his mind to play it perfect. And to be honest, Pep is not that far off of Bielsa's ideas at all.
All these conflicting ideas result in borderline absurd situations like the Thiago - Robben sub yesterday, which for me illustrates perfectly what happens when it all goes wrong. Basically the idea was to sacrifice control in midfield and increasing the speed of transition while preserving Thiago for the Barca tie. All the while changing the tactical setup. Yet the end result is having Thiago not on the pitch to take a penalty, losing the tie and Robben in the hospital.
Point being: The condition in which both teams find themselves in at the moment is the result of made decisions and not chance or accident. Simply a matter of causality.
In delimitation of what Pep did and did not do, Lucho took a different approach: Constant rotation and shuffling the lineup was a huge gamble; the team played sub-par till at least December, Lucho got a lot of flak for it and I wouldn't be surprised if our management was already looking to replace him by summer. He took a huge risk, even individually regarding his future career, and it paid off: At this point, Barca is firing on all cylinders. And that is what I reckon to be an achievement in itself. Which is why I don't think that the current injury situation would in any way belittle a Barca victory over Bayern at this point.