You can do the following to identify the differences.
Check if any of the transactions are appearing under Uncertain Transactions (Corrections needed) of GSTR-1 or GSTR-3B, and resolve them.
Check if any of the transactions are appearing under Not relevant for returns. Check those transactions and include them if relevant.
Check for sales entries recorded in Receipt or Journal vouchers. These transactions are included in the GST returns, but will not form part of the Sales Register.