How does this even happen?!?

I've seen that show before.. It's very sad. Both for the animals and the people living with it (mostly for the animals though). Sounds like that cat you described got in a fight or something, got a scratch on his eye and it got extremely infected. For the black goop could be a horribly bad respiratory infection from breathing in all the ammonia constantly from the other cats feces and urine... I hate to see cats or any animal in thoes kind of conditions... I was watching animal cops phoenix (I think) and this dog had a tumor almost the size of a basket ball hanging off of his neck... It was soo heavy that the dogs head slouched. It was so sad to see. Thankfully they removed the tumor safely and he got a new home :]