The Changeling spy was Pinkie Pie.
Episode 4 reveals that a spy, likely a changeling, tampered with the DISCoRD AI to kill everyone at the facility. Dr. Brown believes the spy is likely an irregular visitor; and the only known visitor present at the time of DISCoRD's activation is Pinkie.
- Jossed with the reveal that Dr. Brown himself is the spy.
The Fall of Canterlot is the reason Twilight lost her memories.
She was involved in the probable battle against the Changelings (Or worse, the rampant turret ponies) and was seriously injured, prompting Celestia (The real one) to send her to Celestia laboratories to recover.
- Confirmed, to an extent, though she actually hit her head while being evacuated from the battle (and she and her friends seemed to be heading for the lab already), and Celestia was too busy being dead at that point to personally send her to the lab.