As a habitual gardener, I can give you a few ideas.
For a very long time, this only happened when seasons changed. So you could have a healthy garden at 11:59 PM on Saturday night, then find plants reverting at 12:01 on Sunday morning, So always save before seasons change. Kind of a pain, but it's necessary. Also, make sure you are at home when the seasons change.There are plenty of times I have come home to several dirt clumps.
If you have taken the time to build a greenhouse, always extend the roof so that you can move plants underneath the eaves. They will remain "sheltered", but won't look as pretty as plants in the greenhouse. Specifically, greenhouse plants will still look normal in the winter while plants under the eaves will be frosted. The reason this is important is that plants in a greenhouse can revert if you are heading into that season. So if you are going from winter to spring, move all your spring plants out of the greenhouse, but under the roof before the season changes. I have had a lot of greenhouse plants revert, Very few that are outside under the roof revert.
Finally. if you are doing anything - harvesting, watering, weeding or fertilizing - save before you start. This is the newest (and most infuriating) version of the bug. It's pretty frustrating when plants randomly revert to dirt clumps just because you are interacting with them. But it does happen. So the best thing you can do is save early and often.
I am not even going to start on the bug reporting process. My job is to play the game, not act as QC. If they want me to be a QC player, they can pay me.
