is it inside? outside? greenhouse?

yellowish leaves usually mean lack of nitrogen. how often did you fertilize and what type of fertilizer?

flushing the potting mix every once in a while is a good thing, but this late in the season way up north where there is less sun and cooler temps, is not an ideal time to flush, as it completely saturates the potting mix.

if your tree is inside, use an oscillating fan to provide some air circulation, it might help with the evaporation process.

Potting mixes commonly grow mushrooms, especially those which are peat based. In most instances, these mushrooms pose no problem. However, the fact that you've been having problems for some time is telling. I suspect that you are using a medium that isn't porous and fast draining enough. What do these mushrooms look like?

How long has the plant been in this container? When was the last time you changed the potting soil?

A porous potting medium can be drenched without fear of waterlogging.