Duplication/Replacement of Tools

Me and a friend have been playing on the Realms server, and for some reason, when we make tools, such as a pickaxe, sword, etc, it will start replacing our other items with even more of the same tool. However, when we use one of the tools, it drains the durability of the other duplicates. Still, this is very annoying and happens at random so we have no idea why or how it happens, The picture for this just shows all of the tools in my inventory, but it doesn't really show what I mean.