Hi @Avishka,
I am not familiar with MYOB Acumatica. The first thing I would investigate is how your middleware creates the AR document, rather than the Numbering Sequence configuration itself.
In a normal Acumatica transaction, the Invoice and Credit Memo can have different document types but their RefNbr is still controlled by the AR numbering-sequence setup.
This is particularly important because DocType is part of the AR document primary key, so an Invoice and Credit Memo are not simply the same record because they have the same displayed reference number.
Also check whether the numbering sequences are configured to use prefixes. As you have indicated from your screenshot that both document types uses the same numbering sequence, then having the same numeric portion isn't necessarily evidence of corruption, although Acumatica's sequence mechanism should normally advance the number rather than reuse it.
Hope this helps you to find the cause of an issue.