I've had harvests appear in the family inventory when I move plants to the family inventory. Have you done this?
Not sure about the harvest vs. harvest all issue. I haven't seen this, but also haven't played since the last patch. In the past when I've used harvest all on my garden, deathflowers are not harvested with everything else.
When you put plants in your inventory, if you did not harvest them first, the game "harvests" them and puts both plants and fruits/vegs in the inventory separately. So if you harvest them first then all you get in the inventory is the plants.
I usually harvest my deathflowers with the one person in my dynasty who makes all the ambrosia, and then harvest all the other stuff with a helper. In the case of putting all the harvest in the family inventory, I had directed her to harvest only the herbs from Granite Falls as the other things weren't quite ready. Instead, the entire garden got harvested and went immediately to family inventory instead of her backpack. Never had that happen before. This is a dynasty file and since I'm only at the first heir, it wasn't that big of a file, (I don't think), but more and more things are going weird with it since the patch. The latest weirdness was having assorted buildings appear in Newcrest that I had never placed there. All of them Maxis builds but I thought it strange.