Usually, when you have duplicate blocks, they are caused from a failed copy operation such as copying something but then having the block positioned in the spot it was copied from as from a rejected action.

Do you know what the prefix "un" means? Duplicate means to make two of something. Un, as in undo, in "unduplicate" means to undo the duplication or simply erase the duplicate.

The point of the warning is simple. Basically, the blocks are in the same space (likely using the same texture) and just wastes memory, disk space, video memory, and causes the game to run slower from having to render the extra block. It's an important warning that you should look into fixing. I've had this once before, but I don't build with blocks anymore.