I have an enterprise with multiple organizations. Under the "seat analysis" tab there duplications of users (same GitHub ID and same Login) from two different organizations within the enterprise.
Referring to Github docs, there are no duplications of licenses:
If a single user receives a seat from multiple organizations in the same enterprise, the enterprise will only be billed once per billing cycle for that unique user. One of the organizations that assigned Copilot to the user will be chosen at random each month to be billed for the seat.
It might be due to this piece of code here.