This is the reply I got back when I contacted them,
Hi Mayor,
I'm sorry you've been having these issues with your Trade Depot. Our team has been actively investigating the cause as a priority.
The Trade Depot relies on online communications to ensure the latest information is relayed between the buyer of your items, our servers and your Trade Depot. If there's a problem somewhere with connectivity (e.g. you were offline at the exact moment the item was purchased by another player or Mayor Daniel or our servers were not able to connect to your game for any reason) it can result in a slight delay updating your Depot, so the items can appear "stuck"! However, it should only take a maximum of 72 hours before the items are successfully cleared from your shelves again.
Our apologies for this inconvenience and thank you for your patience. We are constantly working on improvements in the game and Trade Depot, we appreciate you letting us know.
If you have any other questions or concerns do not hesitate to contact us.