Dupplication Glitch! Items in the chest and in the Inventroy and the same time!

I don't know how and why did happened but I try to explan what I did. Maye you found an reason. So I was in the Nehter. I mined with a stone pickaxe a fossil. After I mined it, I went back to the nether portal and than I went to my chests. It was about 18 to 20 Boneblocks and Because I had other Boneblockes before in it, I know had about 40 Bone Blocks in my chest. I placed them in. Suddenly I herad a skelleton in my garden. I fighted aganist it. I was hiding behind a birch tree and the skeleton was shooting but since it was daytime he burned. After he died I wantet to destroy the tree stump, but then suddenly my game froozed. I coulnd't pressed anything. After I opened the game again I found myself at the point where I had exist the nether with the bone blocks. I wanted to put them in the chest again, but suddenly I had 64 Boneblocks in my chest inseat of about 40 like before. This is bevasue the item stayd in the inventory and was in the chest at the same time because of the crash. Please fix this because it can be up used for dupplication!