You have migrated Customers/Accounts data into the system through Migration Tool and observed that there are few Business Partners with the same name. But, during Migration process of those datas there was no error or warning for the duplicate check.
The duplicate check is only performed if you create business partner using the work centers or views, in other scenarios (like business partner migration) no duplicate check is performed.
This is expected system behavior.
You have to clean up the data first before you migrates/uploads the data to the system.
KBA , LOD-CRM-EMP , Employee , How To