Content Type & Metadata retained in a files coming from a different site collection or tenant

AlbertSP 
This is unfortunately expected behaviour. The "files" are probably Office file formats such as docx, xlsx, pptx etc..
The "files" contain the CT and metadata details from the source in the file itself. When such a file is uploaded to a different site the property promotion kicks in and tries to extract the metadata from the file and capture that into SharePoint columns in the target destination.
Alternatives: not really viable I am afraid.
- after downloading open the files in the client App (e.g. Word) and remove the properties
- disabling property promotion (this may not work on SharePoint Online)
- use Power Automate in your target system to erase metadata
I am not aware of tools that can strip metadata from Office files during uploading/downloading.
Paul | SLIM Applications