Hi @Andrew,
Thank you for posting in this community.
Since we can't reproduce your situation, we need to narrow down the problem and try some things.
So, please kindly provide more information below to let us work further.
1.Please try to access the subsite with the account you logged into the SharePoint migration tool and see if you can access it successfully.
2.You can try migrating this subsite alone to see if the problem persists. Sometimes migration tools have this problem when migrating subsites.
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