Order them by benefit ID, Please.
SELECT T1.source_system_code , T2.council_tax_id FROM CMI_Cross_References AS T1 JOIN Benefits_Overpayments AS T2 ON T1.cmi_cross_ref_id  =  T2.cmi_cross_ref_id ORDER BY T2.council_tax_id
Order by benefit ID refers to ORDER BY T2.council_tax_id;