Doesn't have to be stirred, if build-up is enough it gets to a point where it releases all at once. Many ponds (similar, but not the same, I know) have gone over-night due to this, and is well documented.
Anaerobic Bacteria can be beneficial, though this is usually in the Salt-water scene.
Any dead spot/eddies can build up toxic amounts of by-products/have different parameters that can lead to shock changes, depending on situation and the susceptibility of a particular organism.
A small cave is different than a 1/4 of the tank being cutoff...
Free professional advice take it or leave it... :thup: