During the 2011 and 2012 growing seasons, the brown fuzzy patches were caused by a summer droughts. This year the problem was just the opposite. The summer of 2013 was cooler and wetter than normal. In fact, nut development ran two weeks behind normal all season long. By the end of the 2013 season, many pecan cultivars ran out of time and heat to fully pack the inside of the shell with kernel.
If the expanding kernel does not fully compress all the packing material tightly against the inside of the shell, some of that packing material can adhere to the kernel. Note that the brown fuzzy material is generally concentrated towards the upper end of the kernel half. This is the part of the kernel that fills last during nut development. It seems that time simply ran out for kernel filling as shorter days and falling temperatures promoted nut ripening and shuck splitting.