Dear Bruno,
If you are experiencing the same issue, I suggest you contact the administrators in your organizations and open a support ticket in the Office 365 admin center via the steps in the article for further help. The related support may involve more resources on checking the issue.
To help you in speeding up opening a support ticket, I’d like to summarize the issue as follows.
Issue Symptom:
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When dragging files from the local computers to the subfolders in folders or folders in a site library in SharePoint Online, the file is misplaced in the wrong places.
Issue Environment:
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The site library in the modern SharePoint UI in SharePoint Online
Troubleshooting Done:
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The issue may be needed to be checked on affected customers’ tenants.
Thanks for your understanding.
Cliff