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As we established in the comments section, your problem is not because of wrongly set up virtual environment, but it's worth mentioning the possible solution for others who might come across this question in future.

The problem with virtual env being invoked from other virtual env directory is a frequent symptom of copying virtual env directory from one place to another. This should be avoided! The reason behind that is the VIRTUAL_ENV variable hardcoded in [venv_dir]/bin/activate script. So, always make sure that this variable points to a valid directory.

In order to list packages from a virtual environment only, you need to use --local flag either for pip freeze or pip list. You can find this in the documentation:

-l, --local

If in a virtualenv that has global access, do not list globally-installed packages.

The key phrase is global access. The possible reason why pip keeps finding packages that are outside your virtual environment might be the PYTHONPATH and PATH environment variables. Check them. Whatever you have in those paths will be visible by pip.