I just started a totally new game, a save file I'd been building over the past several months while waiting for the open stair bug to get fixed, and this started to happen.
I just kept playing when the bug occurred, and the dirt piles grew up into ful-grown plants again. I even got to evolve a couple ... and then they reverted again. I don't think it's random. I planted these plants at different times, and I notice that they revert to dirt piles in order of age: first the one garlic plant I started with; then the other garlic plant, the cherry tree, and the one lemon tree I planted a few minutes later; and finally the group of lemon trees I planted the next day. It's really acting as though the "revert to dirt pile" thing is a natural stage in the plant's life cycle ...
So yeah, at this point, I really am going to just treat this as a natural part of the plant's life cycle -- like it's just "winter". (No, I don't have Seasons.) We'll see if I can actually get the plants up to Perfect with them regularly turning into dirt piles every few days.
Some Info:
The expansion packs I own are: Get To Work, Get Together, City Living, Cats & Dogs, Island Living, Discover University, and Eco Lifestyle.
Game packs: Spa Day, Dine Out, Vampires, Jungle Adventure, Strangerville, Realm of Magic,
Stuff packs: Perfect Patio, Vintage Glamour, Laundry Day, Tiny Living, Nifty Knitting, Paranormal,
Kits: Courtyard Oasis
All the plants I've planted are affected. These are: several lemon trees, one cherry tree, and two garlic plants. They were planted after the most recent (July) patch. I believe the "trigger" is actually a timer: the last time it happened, my sim was working out in another part of the lot and not doing anything with the plants at all. I don't know if this timer begins when a plant is fertilised, but it's possible.
I'm not using any mods or cc. I'll check the game version the next time I open it. [Edit: it's 1.77.131.1030]
I'm playing on the Summer Home lot in Windenburg: a 40 wide by 30 deep lot, if I remember correctly. I think the lot traits are Homey, Party Place, and Romantic Aura.
I haven't taken note of any footprint changes; I assume I'm still in Neutral, though I'm not sure. [Edit: Turns out I have eco-footprint gameplay turned off.]
I see a couple of LastException files in my doc folder, but only one dates from within the past week, and I don't think it's related to the bug.
I'm not using a bee box.
The first time I fertilised the plants, it was with lemon; every time after that, it was with garlic. By the time this started to happen, every plant had been fertilised.