Your pond layout sounds really quite good. The 12' depth is a little more than you need but not unreasonable. In fact, you can easily aerate the whole pond efficiently with a 1/3 hp compressor and one diffuser assembly set in the 12 foot depth area. It is very likely that the 12 foot hole is low in oxygen and sort of cut off from normal circulation by the rise you have in the middle. Occasionally, dead water seeps out over the shallow areas and causes minor fish kills. I would think that you have a very easily solvable problem by simply installing a small aeration system. One bubber assembly in the 12 foot area will produce plenty of oxygen to the whole pond.