I am unable to withdraw my items from storage in Calpheon City. When I select withdraw a message pops up that says "There is no item."

it's doing that to me in heidel as well I transferred all my stuff from gilish to heidel. 

When the city has a lot of users it in, it can take a little while to update both inventory and storage. Either wait a bit or disconnect/connect to the server and it will be fixed.