Duplicate Content Detection is not picking up duplicates.
Duplicate Content Detection compares CHECKSUM values of documents against existing documents in Vault.
The Duplicate Content Detection feature compares checksum values against existing documents in Vault. The purpose of this feature is to be sure that the same document is not loaded multiple times into a Vault.
It takes very little to change the checksum value on a document. It does not scan the document itself for similarities. A change in the color of a section of the text, for example, is something that can make two documents different. Saving the same document a second time prior to uploading it to Vault can affect the checksum value.
Vault Document Upload Documentation: Using Duplicate Content Detection