Pardon me posting my video over here (feel free to delete if it's an issue!) but I'm running into an inventory issue with Alpha 6, and being that I ran across it mid-video, it's easiest to explain this way hahaha.
In Alpha 5, items would oddly vanish and when that item was picked up again and actually placed in your inventory, it would trigger the reacquiring of the "hidden" items of its kind; ie., if you accidentally "lost" 5 berries, made space and got a new berry, all 6 would appear in your hotbar. However, in Alpha 6, if your toolbar is totally maxed out and full, it seems these items actually get deleted and are unable to be "retriggered." I tried to explain it around 4:00-6:00 in this video-