This episode sees another re-occurrence of solar flares. They've been conveniently interfering with things since 2005. The Earth's Sun flared on three occasions at just the right time to make the plots of The Parting of the Ways, The Waters of Mars, and The Rebel Flesh possible. Now a different star is flaring at just the right time for this episode to be possible. Of course, in this episode there is an actual explanation: the Doctor is a knew when the flare was going to occur and planned the whole thing in advance. The other flares could just be convenient plot devices for the writers to use, or it could be evidence of some darker conspiracy. I mean, we still don't know who the shadowy figure in the church in The End of Time was, or how the Doctor's mother was moving in and out of the time lock so easily.
We also received mention of two ongoing mysteries in this episode: the woman in the shop and the Doctor's face. The Doctor explicitly stated that very few people in the universe have the TARDIS phone number. The only people who are alive and have the number would be various classic series companions, Martha Jones, Mickey Smith, Captain Jack, Sarah Jane, and UNIT. Now before you say "Sarah Jane's dead", Elizabeth Sladen is dead and Moffat has made no attempt to kill off her character. She could easily still be having adventures with Luke, Skye, Rani, and Clyde. Presumably, the Time Lords would also have the TARDIS phone number, but I don't know what one of them would be doing a London shop giving important phone numbers out to random young women. The Doctor's face wasn't explicitly mentioned as a mystery, but there was talk about not trusting someone with your own face. That could be foreshadowing to the Doctor meeting Caecilius or John Frobisher.
