I have had almost all of these bugs mentioned over the last couple of months or so, so I've been doing some testing.
The main bug I've had is the plants reverting to a dirt pile at different times, some times when nothing is being done to them other times when they are being watered. They will revert to dirt piles and quick growing plants will be ready for harvest again the next morning and slow growing plants will take a couple of day to re-grow. This will keep happening at random it seems but is more likely to happen at the end of the week or during Eco Footprint changes.
Now I have two Origin accounts one with just base game with no packs whatsoever and the other with all packs except the Kits.
I have tried a couple of garden layouts, big, small, just plants and mixes of plants and trees all either bought on the phone/PC or BB mode.
I first tried Base game, no packs of any kind not even the free one, no mods, not even the mods option switched on. No bugs at all for at least 3 in game weeks. Gardening perfect.
I then tried the same but with mods installed continuing the same game save, cleared all my caches put MCCC in and within the first 24 hours in game as soon as it went past 5am everything in my garden started reverting at random and this continued every day until I stopped using that game save.
Next game save I started with my other account with base game, all packs except Kits, no mods, mods option switched off. Again more than 3 weeks in game covering parts of 2 different seasons no bugs, gardening perfect.
Next, same as last time, enabled mods, added MCCC and cleared all my caches, just like before, within the first 24 hours in game, everything started reverting again the same as before.
Both times this happened I mentioned it on the MC Discord and was told it was a known bug, which I already knew. So I thought I'd try it with another mod, so I went through the same process as the last 2 time but this time put in a mod that I can't name here and it did the same thing right away the plants reverted. So it's not a certain mod that's causing it.
I then tried one last thing, did the same steps as before, but this time JUST enabled the mods option, but didn't place any mods in the folder. Same thing happened this time only it didn't happen as quick and not as much.
I have since given up on those saves, started a Rags to riches that relies on selling plants so had no mods in and mods option switched off. When the new update hit on the 23rd I was comfortable enough for money in that playthrough that I decided to check the few mods I use were compatible, put them all back in and play from the same game save after clearing caches and things.
Again, not as fast but all 10 of the in season plants I had reverted at the same time while I had travelled to another lot. Took 2 days and 3 days to re-grow and are now back producing again, for now.
Now after all this I'm 99% sure that for me at least it's the simple process of turning the mods option on that is causing it, or at least making things much worse and also adding different mods are effecting the problem in different ways!
Wow that was a long post!