Frequently Asked Question
First, right click the lone crate and edit it to determine if it's linked to your Sorter. If it's linked, when you edit it, your entire Sorter will be selected. If it's not linked, only that one loan crate will be selected and it will probably show 1 land impact.
IF IT IS LINKED: If it's linked, then link permissions were not properly set so go to the Sorter Menu > Admin > Reset Scripts and be sure to accept (say yes) to any popups you get from the Sorter. After you accept the permissions you can remove any items from the crate you need (Deliver to you if there's anything in it) and once empty you can click the Crate and select Remove Crate.
IF IT IS NOT LINKED: Edit the crate and look in the contents and remove any items you need. Once you're sure the crate is empty of any needed items and you're sure it's not linked, simply delete the crate the same as deleting any prim in SL.