Whenever I shake a tree (cherries and lemons) I am unable to pick up all the fruit that drop. Either that or the objects on the ground just don't register as being picked up leading to having a various fruits on the ground that I can't get rid of, they still have physics too meaning I can kick them around like they're tiny balls

I also experienced this. I found running in around them eventually picks them up though sometimes I'm left with one or two that just won't pick up no matter how many times I run around them.

Same here, first 2 harvests went fine with my cherries. This third time resulted in about 4 I can't pick up