Hi Alex,
Hope everything is going well.
1,Does the account used to access the source site have permissions to read all of those applications? Maybe they are in different scopes, and the account doesn't have all of those scopes assigned? Kindly check the account permissions that you are using for migration.
Required configurations for migration
2, A similar thread for your reference:
SOLVED Migration to new hardware and version, objects missing
Note: This is non-Microsoft link, just for your reference.
Feel free to contact me if you have any concerns/queries.
Best regards,
Simon
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