Shipments/Order going to invoice without physically shipping the order

@mralyea - are the inventory or non stock items set to “require shipment”

They are inventory items that require shipment

this does not seem possible,,, what process is run to create the invoice with no shipment ?  

There is a shipment created, there is just something running that moves the shipment through the confirm shipment status and directly to the invoice status.

do you have scheduled processes?

I would suggest creating case with support so they can duplicate the issue