Why is Stock Ledger stock site not matching with Invoice number site? 

Cause: The user had made the sale return from site code A1 and delivery site code is B1 due to which reference was of a different site. If users change from sites and delivery sites then the stock reflects it in the Stock ledger report.
Remedies: Users should keep the fields from site code to delivery to site code as it is, without editing. Then the stock will reflect sites correctly of Invoice matching with the Stock ledger report.