When you say you clean and change them on a regular basis do you mean the filter media? [sponges and so on inside]. They do not need changing just rinse the in tank water and put them back in the filter.
The filter media is where the good bacteria that eat the ammonia grow and if you over clean them you will get a ammonia and or nitrite spike. This in turn makes the water toxic to the fish and could be the cause of the bubble eye. Bubble eye is generally seen in poor water conditions.
Lisa x