QB Issue Resolution:

Yes, credit note number takes the invoice number sequence. If you want to have the different number for credit note, request you to please enter the number manually.

Resolution for Issue 'IN: how do you number the credit note? it seems to take the invoice number sequence' available: Yes (Solved).
Source: Intuit Community forum.

IN: how do you number the credit note? it seems to take the invoice number sequence: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

Support for credit note
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Error Recovery for credit note [Canada]
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