If you are on PC, put them into your inventory, drag and drop them on to each other to stack them, and put them back. On cosole you may need to deposit them into you personal bank and pull them back out. (Keep track if you have the same item in your bank.) That should probably stack them and you can then put them back in the guild bank. My understanding of how they don't stack in the shared guild bank is to prevent a duplication error that was exploited early on.