Marketplace administrators can also post listings and offer their own products/services. This would mean that in some cases, the listing author and the marketplace admin are the same user and therefore have the same PayPal account. When someone pays for the service, rental, or product involved in these listings, both the payment for the listing and the commission will correspond to the same user. In that case, the commission fee isn't transferred.

In normal transactions, PayPal charges a fee both from the payment to the seller and from the transfer of the commission to the admin. You can find out more about how this works in these two articles of our help center:

In a transaction when the seller uses the same PayPal account as set up in the marketplace's payment settings (they have the same PayPal account), the second movement of money (the commission from the seller to the admin) is not needed, as it's not possible (or useful) to move money from one PayPal account to that same account. 

This happens when the PayPal account defined in the marketplace Admin panel (Admin panel / Payments) is the same that a seller's (User settings / Payments).

In this situation, the commission wasn't transferred at all to avoid unnecessary PayPal fees.

No, that money didn't disappear. It remained on the seller account, so no money has been lost. In fact, some money has been kept from avoiding PayPal's fees.