He has not won the CL with Bayern Munich and ManCity in seven years, even though he had virtually unlimited financial possibilities. He has so far only succeeded in Barcelona because he knew the club and the mentality for a long time. Besides that, Barca was a well-rehearsed power at that time (even before Pep was coming). He may be a great person and an obsessive coach but he has not yet proved that he can achieve great international success with other teams than Barca.
The statistics of the match tells a own story. Losing the match 1 - 3 with having an overall ball possession of 67% (33% Lyon).
My theory : he overthinks and tries to micromanage to extreme, which I think should not be done at the level he does, also his overload way of playing is creating to much congestion in the final 30 meters of the pitch and if a team has quality, discipline and knows how to defend you actually have harder time scoring then by playing more direct football.
Another important factor I think is his choice of players, he likes players that are too technical, good with combinations and puts less focus on strenght,power and clinical finishing in a player when it comes to attackers and forwards is general. You get a lot of chances that way and you create a lot chaos and that works great against normal teams in a league, but when you get to high end matches and you have teams that are equal or stronger you start to see problems.
So his selection is also a problem in my mind.
I mean Zlatan had to leave from Barca because he didn't fit his style, cmon... Also Mandzukic whom was doing great things for Bayern had to leave because of him too.
I know this is a tip of the iceberg, but I firmly believe this things I wrote are correct or very close to the core reasons why his teams and his style and approach to football has problems on the high end. You need to have perfect players and perfect chemistry for it to work and that is extremely hard to achieve when it comes to that style of playing football.