Hi @Kuronuma
Could you please tell me, when you view the file in the SharePoint site, you see two options [In channels] and [In site library], which is not what you want.
However, according to our official documentation, we regret to inform you that this behavior is by design.
Whenever you create a new team, a SharePoint Online site is created to store your documents. This means that every time you share files in the team, they will be stored in the associated site in SharePoint. The exact location depends on which Team channel you share(d) them in. By default, there's a General channel (which can't be deleted), and the files shared in this channel will be stored in the SharePoint site, in the Documents library, within the General folder. If you create a Team channel called "Project A", files shared in this channel will be stored in SharePoint under the folder called "Project A", and so on.
If you need to control who has access to your files, you can add or remove users from your team, which will add or remove their access permissions on the SharePoint site.
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