It's because their main focus was the CL, Rafa Beñitez said so himself. They put out their main resources for the CL games, and when it came to saving some players on the premier league games to keep them fresh and good for the CL games, they did that almost every game. Mainly it was because they were still in a construction phase of the team, and weren't as solid as they are right now, some sacrifices had to be made in order to try to accomplish something that year. They played a phenomenal footbal in the CL but were seriously underwhelming in some Premier league games. I think that's the case with Bayern this year, the pattern seems almost identical. They had a massive loss this week against Wolfsburg, but on CL they are playing some really good games.
Current PC Build
CPU - i7 8700K 3.7 GHz (4.7 GHz turbo) 6 cores OC'd to 5.2 GHz with Watercooling (Hydro Series H110i) | MB - Gigabyte Z370 HD3P ATX | Gigabyte GTX 1080ti Gaming OC BLACK 11G (1657 MHz Boost Core / 11010 MHz Memory) | RAM - Corsair DIMM 32GB DDR4, 2400 MHz | PSU - Corsair CX650M (80+ Bronze) 650W | Audio - Asus Essence STX II 7.1 | Monitor - Samsung U28E590D 4K UHD, Freesync, 1 ms, 60 Hz, 28"
