If all of your contributions to the 401(k) were Roth contributions and there were no employer matching or profit-sharing contributions which would have been made to the traditional account in the 401(k), that code 8 Form 1099-R is simply wrong and needs to be corrected by the plan administrator. That form should have codes 8 and B, and the only amount that should be in box 2a is the amount of taxable gains, that are part of the gross distributed from the Roth account in the 401(k).
Yes, a proper correction would be for the plan to issue a corrected code 8 From 1099-R showing $0 distributed and a new code 8B Form 1099-R showing the gross distribution in box 1 and the taxable gains in box 2a.
You understand this better than most in a similar situation who post here and seem to understand it better than the HR department and plan administrator.
