You are indeed right. This shouldn't have happened, as the duplicate was set to NFE (not for extraction), and should not have been part of the game database. I'll raise this issue with SI internally.
Need to edit my reply here, as I looked deeper into the issue. The NFE tag was set after the data was extracted for the public beta, but before datalock. So in other words, the duplicate will not appear in the full release, only in the beta.