Why Pep Guardiola's time as Bayern Munich's manager was a failure
Pep Guardiola is widely regarded as one of the best football coaches of all time and his success with FC Barcelona and Manchester City has cemented that position. He is a manager who has become known for playing exhilarating football and winning at the same time, which is why he has become extremely influential to a lot of coaches all over the world.
However, things didn't work out at the end. Guardiola coached Bayern from 2013 to 2016 and won the Bundesliga with extreme ease during those three seasons but failed to win the UEFA Champions League. Why was that? There are some reasons for that.
The playing style
A major aspect that a lot of people tend to forget is that football teams don't exist on a vacuum. When a manager arrives to a club, the squad has a certain shape and a certain history, which is something that Guardiola had to deal with as Bayern had recently won the treble and were cemented as the best team in the world.Furthermore, this Jupp Heynckes-led Bayern won everything in the 2012/13 season on the back of intense pressing, a very balanced structure, and the ability to play with and without the ball. This was a side that was very flexible and had a lot of efficiency and a "matter-of-fact" approach to the game that perhaps wasn't very romantic, but was very effective and the proof is in the pudding since they were the first Bayern side to win a treble.
Guardiola, however, wanted to implement his own playing style of possession, which makes sense because that's what he was hired for. It wouldn't make sense to bring him in and ask him to do something different.
However, Guardiola's style wasn't a good fit for that Bayern side at the time. Yes, they won the Bundesliga during those three seasons but they had much better sides when compared to their competition, which was complemented by them weakening the opposition, such as when they took Robert Lewandowski and Mario Götze from Borussia Dortmund.

"When I speak to supporters, they tell me that when Jupp Heynckes was the coach, they could feel that it was Bayern's DNA. We also defended - we didn't always attack and have ball possession."
"People said 'Guardiola: a great coach, but we couldn't feel our DNA in his game'. That sounds very strange, but maybe it was a little bit of a problem sometimes. Then in the semis of the Champions League, small things make a difference, and you either reach the final or you don't."
Lack of adaptability
Bayern were a tremendously talented and strong side with Pep Guardiola but they weren't the objectively best squad, which came at full display during the three UEFA Champions League semifinals they played with the Spanish managers. That was when it was shown that the team couldn't rely on just raw talent and needed something extra, which wasn't at display during those three semifinals because of a lack of adaptability.Perhaps the best example of this were the semifinals of the 2013/14 season against Real Madrid. Carlo Ancelotti's made quick work of Guardiola's possession-based style through counterattacks by Cristiano Ronaldo, Angel Di Maria, Karim Benzema, and Gareth Bale, with the Germans losing the second leg by a now-historical 4-0 score.
While they lost the next semifinals by a 5-3 score over the two legs, Barcelona's triumvirate of Neymar, Lionel Messi, and Luis Suarez was too much for Bayern to handle. And Atletico Madrid finished the trifecta the following season with staunch defensive performances, which is something that Bayern never managed to adapt to.
The nature of small margins
The truth of the matter is that football is a game of very small margins and things don't often go as one may plan. This may sound a bit cliché but that is something that a lot of football fans need to understand because historical moments can be defined by very small decisions.Ultimately, Pep Guardiola's Bayern Munich side struggled to perform in the small margins of the matches and never got the results they wanted. Perhaps the most prominent example of this was against Atletico Madrid where they were dominating the Spaniards during several portions of the two legs but never managed to break them down.
This is something that can happen a lot in football and sometimes teams benefit or suffer from this. Bayern themselves benefitted from Borussia Dortmund's defensive mistakes for Arjen Robben to score the 2-1 goal that would give the UEFA Champions League in 2013. It happens and Guardiola's team suffered that.
However, that doesn't stop this project from being a failure. Guardiola was tasked with creating a dynasty at Bayern, although there is an argument to be made that he wasn't the right fit for this project. Be that as it may, it is still widely regarded as the lowest moment in the Spaniard's coaching career.