A good place to start is the field you have specified for "Product Inventory" which you can find in Add-On Manager / CartThrob Pro Configuration / Products - it is the fifth field down in a channel definition block there. If this field is set in your custom channel, check to see what kind of field this is set to be (should be a regular text field), and what values it has. If this field is, or appears to have value 0 then you'll get stock out errors...
Another place to check is the option in Add-On Manager / CartThrob Pro Configuration / Orders for "Update Product Inventory When Editing Order" - if you do not want inventory warnings at all, simply de-select this option.
HTH.