How do I prevent duplication data uploaded to MySQL database from a CSV or Excel file upload?

you may

1. use unique keys
2. before insert triggers in the MySQL
3. write a program, maybe PHP, to perform Pre-Insert tasks
4. maybe more

In one migration project from a Tailored Oracle Accounting System to SAP, I had done the insert using PRO*C programs for the export (where there were possible checks) and the Impor Utility of SAP).