Q:

How to raise concerns about ethical issues in UX design?

Just wondering if there are any examples of processes or standards in place within companies to raise ethical concerns related to UX design practices that anyone is aware of. I don't think there has been enough discussion around the topic, given the emphasis that has been placed on (and attention given to) social and corporate responsibility and social enterprises.
I would like to know which department and what positions are usually assigned this responsibility within a typical organisation.
The reason I have asked this question is because I don't think the HR or legal department of an organisation has enough knowledge to be able to help define the standards or best practises for the company, and that their view is going to be biased or aligned with business needs and requirements, which can be in conflict with the users' best interests. The other reason is that product owners and managers or people that the UX designers normally report to also don't have enough visibility to the design process and outcomes to understand the issues at stake.
I liked this quote from Saint Francis of Assisi (1181-1226), which summarizes my view of how we should be able to deal with ethical issues within the workplace:

If a superior give any order to one who is under him which is against that man's conscience, although he do not obey it yet he shall not be dismissed.

A:

I don't think this is specific to UX
Ethics violations, reporting and whistleblowing are no different for UX than they are for any other part of a business.
The best practices for organizing risk management nowadays (post global financial crisis) include:

Forming a Risk Management committee on the Board of Directors (this is often merged with the Audit Committee function)
Providing an Enterprise Risk Management or ERM framework for the business that is overseen by top management and ultimatly by the board.
Creating an internal audit function that reports to the CFO and also directly to the board. Internal audit covers not only financial malpractice but also ethics and business policy violations.

Part of the internal audit function includes providing adequate whistle-blower channels and protection.

How does this relate to ethics reporting?
If these best practices are followed:

The Enterprise Risk Management framework should provide for multiple layers of ethics reporting from line employees all the way up to the board:

Typically, employees are encouraged to report ethics violations upwards in the line of business (manager, then director, etc). Failing a satisfactory response, employees have access to whistleblower hotlines (where they are guaranteed protection) and ultimately directly to the audit committee of the board and the board itself.

If employees are concerned about retaliation, there are external government and NGO organizations set up to handle corporate ethics whistleblowing.  If you're interested I can cite a few.

The internal audit function should provide downward monitoring of ethics issues by issuing standards, conducting periodic audits, and (in larger companies) engaging 3rd party auditors to assess the quality of ethics frameworks and also to interview employees periodically and confidentially.

The corporate structures for ethics and risk management are complicated by nature, because they have to work across a broad frontier of potential ethics and risk violations so this is typically handled via multiple paths and multiple layers.

