It seems to be related to the update, I didn't get EL, but some of the plants, mostly trees, seem to grow back to sprouts overnight, I figured it might have been the time when these plants would usually "spawn" harvestables. I honestly thought it was seasonality issue, that may have not been the case judging by everyone's post here.
There was once when my sim weeded a plantain tree, it was suddenly reduced to a pile a soil!(as if just planted, again)
PS. If you opt for a dirty workaround, shift clicking the plant with testingcheats on will let you set the growth stage :smile: