The main reason why a record will have multiple attachments with the same name on a record is that the user that the MID Server uses to connect to the ServiceNow instance, doesn't have permission to do the attachment to the specified record.

The user must have a role that enables both creating an attachment and deleting an attachment.

For an example.

MID Server User is : mid.user

A PDF is being created and attached to a custom table my_table

The user, mid.user, needs to have any roles needed to create an attachment to my_table.  

You can test this out by Impersonating the MID Server user (in example it was mid.user) and attach and delete an attachment from the table in question.