Some new items cannot be stack with older items of the same name (example makeover kits, pristine fractal relics, blade shards, etc).  From Anet employee Lauree, if you run into this do the following:

1) Move the “Account Bound on Acquire” items from your bank into your inventory.
2) With the items in your inventory, either log out of the game or change maps.
3) Once you log back in, or once you complete your map change, you will find that your items are now “Account Bound” and that they now will be stackable.

Anet has asked any guild to report issues they are experiencing.  I made an official post for us on their forum thread. This post will be taken off of the homepage when the bugs are resolved.  Thank you everyone :D
https://forum-en.guildwars2.com/forum/support/bugs/Issues-with-the-Guild-System-Post-here/page/8