In process_mpp.py in line 658 (if pops[state_i] > pop_thr and qmin > qmin_thr:), only the population of one branch is tested. This may lead to macrostates (state_j) with a population below pop_thr. The fix is as simple as if pops[state_i] > pop_thr and pops[state_j] > pop_thr and qmin > qmin_thr:.