Since Sage v22 (we're now on v29) there has been a feature to avoid duplicate payments to the same supplier built-in to Sage Line 50, although it is rather limited in it's scope of analysis.
You can activate the function by:
Clicking Settings, and then Company Preferences, and then click on Parameters.
Select the Check for duplicates in Customer batch entries and Check for duplicates in Supplier batch entries, as you see fit and the Sage Line 50 duplicates payment detection will be activated when you click OK to complete the process and return to the Sage Line 50 application.
The main thing to remember is that this is a very simple detection process and analysis system. Once activated it will detect duplicate payments made to the same supplier for the same amount, and being a double entry system, a duplicate invoice number will not be permitted, but it will not check the amount against previous invoices for that supplier as the detection was not initiated when they were input, and so are not flagged to be checked for duplication. This obviously applies to payments and invoices processed before the system supported detecting duplicates.
Sage does also not check against payment references for duplication as the reference has always been considered something that can be applied many times but this may change with later versions.
Nowadays SageOne loads transactions directly from your bank online, and so duplicates are less likely to be made as the cashbook is always up-to-date.