All of the Bundesliga games last night had more than three goals in each of them;
Leverkusen won against St.Pauli with four goals to none, Frankfurt against Gladbach with three goals to none, Hamburg against Union Berlin with three goals to two, Hoffenheim against Freiburg with three goals to none, Bayern against Bremen with three goals to none and Stuttgart against Cologne with three goals to none.
Another surprising thing is that all of the winners of last night game except Bayern Munich were playing at home!
I think you're mistaken the number of goals. When you said all the Bundesliga games yesterday had more than three goals, it means the scores are from four and above and we shouldn't be seeing scoreline like three to nill as you explained in your second paragraph. Bundesliga had six matches played yesterday and only three matches had a score of more than three goals while the remaining three matches had exactly score of three goals. I don't know maybe you posted before the final whistle but Stuttgart against Cologne game did not end in cleansheet in favor of Stuttgart, Cologne put one goal passed them to make it three to one before the final whistle.
Bayern Munich is too strong in this league that they don't respect your home. It doesn't matter whether they are playing in your backyard or you're playing at their home, they will beat you mercilessly regardless. The only thing that's stopping Bayern Munich from lifting the trophy is just time.