Plot hole: Near the end of the episode, the part-human Doctor is said to have all of the memories of the original Doctor. If this is true, then the part-human Doctor should remember the time the original Doctor spent with Rose, so shouldn't commit genocide or need Rose to help him to not be a man of killing.
Plot hole: Davros said that the reality bomb would destroy all parallel universes. He fails in the Doctor's universe, but the Doctor said in an earlier episode that every decision creates a new parallel universe, like if Donna had walked out of the TARDIS with Jack, Rose, and the Doctor. She wouldn't have imbued herself with Time Lordness, so Davros would have succeeded. This means that all the universes, including the Doctor's one, should have been destroyed, because if the Reality bomb only succeeds in one universe, it would destroy all the others as well.
Plot hole: In this episode, the Doctor is said to have died during the events of "The Runaway Bride." As a result, he was not able to prevent the spaceship Titanic from crashing in London. It is later shown that southeast England was obliterated by the explosion. This falls far short of what the Doctor mentioned in "Voyage of the Damned", wherein he frantically repeated that if the Titanic crashed, the drive's explosion would wipe out all 6 billion people on the Earth (that's the entire human race at the time of the show's airing).
Plot hole: After getting out of the Pyrovile escape pod, the Doctor and Donna start running back to Pompeii. In the process, they are somehow able to outrun what appears to be a pyroclastic flow. Pyroclastic flows can reach speeds of up to 700 kph, and should be impossible for them to outrun.