Wabbajack uses the Nexus Mods API in order to automatically download files (only available with a Nexus Mods Premium account). The API has a limit to restrict the number of automated interactions a user account can have with the site in a given time frame in order to help mitigate the site being impacted by massive volumes of requests.
If you run out of API calls you will have to wait until they reset or manually download missing mods and put them in your downloads folder.
API allocations reset daily at <t:1731024000:t> (Midnight UTC).
This is a limitation imposed by Nexus Mods and cannot be circumvented or changed by Wabbajack.