Why do I have invoices with the same number?

These are documents of different types (invoice and invoice-receipt), with each type of document following a sequential and chronological order. That is:

Invoice seriesname/1, seriesname/2, seriesname/3, and so on.

Invoice-receipt seriesname/1, seriesname/2, seriesname/3, and so on.

Credit note seriesname/1, seriesname/2, seriesname/3, and so on.

This is the correct behavior and in accordance with the rules of the Portuguese tax authority.