I still get the dirt pile bug and I can't figure out what causes it. I no longer use the great soil lot trait, I harvest before tending the garden, and it doesn't happen when I fertilize the plant every time.
I had it happen when I have only one plant, (one or more plants) in planters or in the ground (inside building or outside) and in the middle of the day when my sim is doing something else on his or her lot, I'll notice that one or more plants converted back to the dirt pile. I had it happen sometimes after fertilizing, after evolving, in the middle of the day, (after going into build mode and adding decorations) and while tending the garden.
I think I'll try to get a plant to perfect where it stops evolving and see it stops converting back to the dirt pile. (And if that doesn't work, I'll turn off the EL environment effecting in the settings).