Hubber has two major functionalities: 1. Calculating "cohesiveness" of input gene sets in a functional network; 2. Calculating the association of all the genes in the network to each of the input gene sets.
Functionality (2) appears to be OK, but not (1). The incorrect calculation of cohesiveness comes from counting edges between genes in the input gene set twice, leading to wrong values for 'hubbiness'. ['cliquiness', on the other hand, is looks fine.]