The email package has an issue with extracting the attachments from the email if the email is sent with the Outlook application with .msg files.

When I'm sending an email from the Outlook app by attaching .msg files to the email, the recipient receives the email but instead of .msg files, the email contains .eml files. So Outlook auto transforms the attached .msg to .eml.
When I'm trying to read and extract attachments with the email package by using the Message class "get_payload" method, the extracted data for the mentioned attachment doesn't contain necessary information like "content-disposition" or "filename", so working with that attachment is impossible.

For all other .eml files everything works fine. The issue exists only in the case of transformed .eml files. However, that .eml looks like any other eml file in the received mail.

That file appears to be a binary file?  By itself it isn't enough to reproduce the problem.  Can you provide a complete script as well as the email message you are parsing that demonstrates the problem?

By "looks like any other eml file", are you including the MIME headers associated with the part?  Because it is the MIME headers that contain the information you say is missing.  Mostly likely, outlook is not supplying that information for these transformed eml files.  If you can supply a copy of the actual email message you are parsing, we should be able to confirm that.