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It seems you did not distribute the problematic package to distribution point or you have delete it from DP, you may need to redistribute the problematic package to distribution point.
Then re-run the content lib cleanup tool.
For more reference:
https://www.prajwaldesai.com/content-library-cleanup-error-this-content-library-cannot-be-cleaned-up-right-now/
And it seems it's a known issue:
https://learn.microsoft.com/en-us/mem/configmgr/core/plan-design/hierarchy/content-library-cleanup-tool#known-issue
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