Yes. IRP can reject an invoice.

IRP will check whether the Invoice was already reported and exists in the GST System. (This validation is based on the combination of Supplier’s GSTIN-InvoiceNumberTypeOfDocument-Fin.Year, which is also used for the generation of IRN). If the same Invoice (document) has already been reported earlier, IRP will reject it.

Will also perform Certain other key validations on the portal. In case of failure, registration of Invoice won’t be successful, IRN won’t be generated and will reject Invoice along with relevant error codes (which give an idea about reasons for rejection.)