Recently I have been growing almonds for a friend in LoE and some of them will not stack with the majority. Last night one of the developers looked into it and saw that the metadata on the "bad" almonds did not match the metadata on the normal ones. The game client cannot set the metadata so something is off somewhere.
I tried this yesterday and naturally the bug did not occur. I am going to try again today in an attempt to catch the bug. As usual, I will start with no almonds in my inventory and see how things go.