I just caught the bit where Jack went though deleting all of the Doctor's records from the Torchwood Three database right after the Cardiff quake.

And I realized that, yeah, he really needed to delete the CCTV footage as well. Not just for the fact that it's the Doctor hanging around Cardiff, and a "second" Jack, but they also made off with the Mayor of Cardiff! And Jack had to have covered that up since no one was making any noises about the Doctor being a kidnapper of government officials.