There can be several reasons for duplicate publications appearing in your RPPR.
In many instances, this occurs because publications have been entered multiple times in MyBibliography. If this is the case, you will need to merge them so the duplicates are no longer visible. Detailed instructions here: https://publicaccess.nih.gov/my-bibliography-faq.htm#I.3.Deletingduplicates
If your publications are not duplicated in MyBibliography, it is likely that the grant you have associated with the publications has additional PIs who are also reporting on the same grant. If this is the case, proceed with report submission. Per the ERA Commons help desk, "Your grant is a Multi-PI grant and that is the reason you are seeing duplicates of the publications. The system is behaving correctly and this will impact the submission process."
Contact the ERA/RPPR help desk directly here: https://www.era.nih.gov/need-help