From the documentation:

The docker cp command assumes container paths are relative to the container’s / (root) directory.

^Source:

This means that, when your docker exec [CONTAINER] ls is affected by the WORKDIR, your docker cp is not.

What you should do from there is to run:

1. docker exec [CONTAINER] pwd
2. Use what this yields you in the docker cp command to have a fully qualified path to use in you docker cp command

e.g. from the httpd image:

$ docker run -d --name httpd httpd

$ docker exec httpd pwd
/usr/local/apache2

$ docker exec httpd ls
bin
build
cgi-bin
conf
error
htdocs
icons
include
logs
modules

$ docker cp httpd:/usr/local/apache2/conf .

All this because the httpd image defines a WORKDIR on the folder /usr/local/apache2.