That's odd as my gardening has been going fine. If I was you I would make a new sim and see if it is happening to them as it could be a glitch or you might have a bug that needs to be reported and unless you are fine with no plants growing produce then you might have to restart a new game. The same sort of thing happened to me but items kept reappearing in a sim inventory even after I sold them.
For your evolve plant problem, is your plant sparkling? As that tells you it is time to evolve it or it might be related to this glitch/bug. Again it might be an idea to try this out with a brand new sim in a new game and see if it happens there.