During the verification OAMG-3436 I found an incorrect behavior (pstodulk@redhat.com confirmed it's legit bug in leapp):

Verification of the container, test case copy file first, then overwrite with dir:
First, file is copied from host to the container. Then empty directory, with same name as parent directory of file within the container, is moved to the container. After that, the file is no more in the container (parent directory was overwritten with copied empty directory).

The verification test for that is already created: https://gitlab.cee.redhat.com/oamg/jats-leapp-repository/-/blob/oamg3436a/src/ver/oamg3436a/test