Because even when programmes are made by independent companies on behalf of the BBC they still need to have been signed off by the BBC before they’re aired.
Its a compliance issue that it wasn’t picked up, and the BBC would never redirect that blame because ultimately the sign off sat with them.
Its not that there’s no separation between independent TV producers and broadcasters, but independent producers will make content for multiple broadcasters - they might be making programmes for ITV, Channel 4, streaming platforms plus the BBC at any one time.
Yes they’ll be contracted legally to supply content under the editorial policies of those individual broadcasters, but they’re not tied to one.
So in some ways you’re right, the audience should see no difference between a programme made by an indie for the BBC but that’s only because they’re contracted to make that programme in a BBC format.
Loads of tv programmes are made in this way, C4 don’t make anything in house except news I think.