Never been in a manure pit. We did not have them on our farm. But how can a farmer with a manure pit not know of the high potential for toxic/lethal gasses in them.
I work for the USDA-Natural Resources Conservation Service and we help a lot of farmers build manure pits. Manure gas safety is strongly emphasized and warning signs are posted all around. There are safety rules like don't agitate on a calm day and NEVER enter an enclosed pit without a SCBA and a spotter. But sometimes people forget, sometimes something happens.
There was an incident in central Pa. about 3-5 years ago. Grandpa was agitating the pit and was fine. But he walked around to a lower level and there was his grandson passed out on the ground. He dragged him to safety and the kid recovered. As near as anyone could figure, the gas (which is heavier than air) had settled at a lower level. Grandpa was tall enough to be in good air, the kid wasn't.
Cooperative Extension, Pa. Dept of Ag and NRCS take every chance we get to remind folks about manure pit safety. But bad things still happen.
Condolences to the family.