I have this only happen to me when my sims travel for a slightly longer outing (the Finchwik Fair for example) without previously having harvested their crops. While it is somewhat annoying, I assumed it was by design so you don't miss the next harvest.
Further discoveries:
Using planters seems to have some effect.
I moved some plants from one of the new garden patches into a planter (still outside) and on reloading the game, these harvestables now go into the HH inventory - they didn't when they were in the garden patch. I also removed the floor from my indoor greenhouse and moved some plants from indoor planters into the ground (sheltered) and the harvestables no longer went into HH inventory.
However, my dragon fruit plants have been outside (in a garden patch) the entire time and they are one of the plants that is affected by this bug.
It only seems to be certain plants as well, I have some large planters with 4 plants in and only some of them are affected by the bug. e.g. I have black bean, raspberry, chocoberry and blueberry in a planter, only the black beans go to the HH inventory.
Plants that are consistently affected in my game are: onion, potato, tomato, black bean, crocus, dragon fruit, lovely mushroom, death flower, soy bean and spinach.
