Short answer: 

email.fileattachments = null;

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Long answer:

If you use the value METADATA_WITH_BODY you'll have duplicate attachment as explained in the doc.

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.i.e: Messaging.SingleEmailMessage email = Messaging.renderStoredEmailTemplate(templateId, recipientId, opp.Id, Messaging.AttachmentRetrievalOption.METADATA_WITH_BODY);

System.debug(email);

=> You'll see that both entityattachments and fileattachments are filled, which is why you have duplicate

So you just need to remove one of them (and doc says remove fileattachment)

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