For a while, I've had the Bean There, Done That quest, which asks you to plant 3 beans and pet/water 3 seedlings through the sapling phase. I finished planting the beans and have petted/watered plenty of seedlings past the sapling phase, but for the section of the quest, it still only says 2/3 on my log. I don't know if this is because it has to be the three exact trees you planted, which would seem strange, since those are long gone.