The change to shaking trees to get fruit makes any trees you may have planted on the left edge of the greenhouse lose fruit. Single fruit just float away and disappear, if you wait 3 days so there are 3 on each tree you can get 2 of them.

I loaded up a copy of a saved game and tried to plant new ones farther out from the wall, but it seems that it is no longer possible to plant them outside the soil area, I guess that was a bug and not a feature. :) I always thought it was kind of strange that you could plant trees on the solid floor of the greenhouse.....

Also planting a fruit tree on tilled soil in the greenhouse results in some seeds being put down, that does not happen on tilled soil on the farm. You also lose the sapling you just bought, so if planting fruit trees in the greenhouse now make sure you use the pickax to de-till the soil before planting.