For the gardening issue, try going to Buy Mode and moving the plants around the lot a little bit. I haven't had any issues after Patch 1.39, but that solved the gardening issue for me after installing Patch 1.36 (or whatever the previous one was called).
Hmm, do you think that would also address the fact that the "harvest" action in public spaces are also cancelled? I tried moving the family with and without their house, but no matter what I did, the gardening was glitched. I finally gave up on them and started the original fairy and witch sim in a new game without all their kids and skills, and starting anew. I might consider moving the plants around though, but I was wondering if you had also had that glitch when harvesting in the wild...otherwise I think this game is going to be lost unless I want to get rid of the garden.
To be honest though, there were lots of things about the file that seemed to get worse and worse. Bonehilda started acting erratically, always taking food out of the fridge and setting it on the counters and floors. Every time one of my Sims tried to throw out food or other trash, they would get a routing error in front of the garbage pail for no apparent reason - when I replaced the garbage pail with a trash compacter, they would ALWAYS stop and shout at me where the garbage pail WAS, and then proceed to the trash compacter. It's disappointing to lose all the progress I made with them, but starting over has some appeal as well. It was just so frustrating because the male reached the highest witch and alchemy skill, at the top of the alchemy profession, and he only needed to learn 4 more recipes. My fairy woman was a level 10 fairy and gardener, and nearly to the top of the gardening profession. Hey ho!
