A detailed breakdown of earnings is only visible after creating the payout request. If a refund has taken place it is reflected immediately in the estimated amounts that are displayed.
Is there another fee I am not seeing/I am not aware of?
If the user had a itchio share configured on their account at the time of the bundle then it may also contribute to the reduction of the net revenue: https://itch.io/docs/creators/payments#open-revenue-sharing