Brown stains/trails on the exterior of the hive is indication of nosema/disentery. If they are strong enough, this will clear up come spring when the weather gets better. If they are not, you could consider treating then with Fumagillan in sugar water if you have access to it.
Some have also claimed that cider vinegar helps as well. I have no experience with using cider vinegar on hives showing symptoms, but have tried it as a preventative measure.