Department & Sub-Department not reflected in reports

I have noticed that even though we have SKUs set up with both departments and sub-departments, they are not always shown on the reports. Sometimes on the report it will show the department and/or sub-department field blank for SKUs, even when they have a department and sub-department. I dug further and found that when this happens, these SKUs do not show up on a “Sales by Product” report filtered to their department and/or sub-department either. This is becoming a problem for us, as we use departments and sub-departments to track sales for different areas of operation that need to be kept separate in our accounts. Has anyone else had this issue? Any thoughts on what to do about it?