The run differential can be misleading when you have a few really lopsided losses.
In the Brewers case they win more than their share of the close games and some times have conceded and surrendered a lot of runs when games were out of reach. Like giving up 18 or whatever it was against the Cardinals.
My biggest concern all along has been that the weak offense produces almost no easy wins meaning that the bullpen has to be used heavily in almost every win. Look at their day by day results and there are precious few wins without saves, especially in the last two months, and most of those require 3 or 4 relievers. That eventually might take a toll, and Peguero seems to be showing signs of it the last week.