Jack Harkness uses the alias 'Owen Harper' when identifying himself over the undead body of the suicide bomber. Owen Harper was the name of Torchwood's medic during the first two seasons while the show was still running on the BBC.
When Gwen asks Rex to say something to demonstrate the functionality of the I-5s and lip-reading software, he gives his full name and adds that he is representing the Central Intelligence Agency. However, the software replaces "representing" with "resenting."
Jack comments that the warehouse is "bigger on the inside than the outside," referring to the TARDIS, the time/space vehicle piloted by the Doctor. Jack met the Doctor in World War II and traveled with him for a while, and gained immortality as a result of his travels.
When Oswald picks up the baby at the hospital, it only has one sock on, yet for the rest of his speech the baby then has socks on both feet.
Jack uses the alias "John Smith" while speaking to Frumkin in the park. While "John Smith" is a commonly used alias and a common generic name, it is likely that Jack's use of it in this episode is a reference to his friend The Doctor who has consistently used the alias in many of his regenerations.
When the hospital representative opens her folder and says "I have set up a schedule," she opens her folder but it and the papers inside are upside down.
While Rex Matheson is recording, we get to see through the viewer the battery and time left to record. When he starts, the battery is at 54 minutes and the tape is 1 hour 23 minutes. After he goes outside and continues to record for awhile, we again see the timers again and they are still the same (54 minutes battery and 1 hour 23 minutes on the tape). Yet, more than a minute has passed.
In the episode "The Categories of Life," Rex Matheson is recording the events at the module. The viewer is able to see the battery and time left to record. Throughout the episode it stays at 54 minutes battery time and 1 hour 23 minutes time left to record. At the beginning of this episode the battery time is still 54 minutes and time left to record is 1 hour 23 minutes even with him recording the death of Doctor Juarez, multiple modules, and his recording information about his being in Torchwood.
Jack mentions that the Parasite he is hunting is a member of the Trickster's Brigade. The Trickster is a member of the Pantheon of Discord who altered the histories of individuals in order to change the overall timeline for the worse and feed off the energy caused by the chaos. The Trickster was a recurring villain on the Sarah Jane Adventures where he consistently targeted the Doctor's oldest companion, Sarah Jane Smith.
A different member of the Tricksters Brigade previously appeared in the Doctor Who episode "Turn Left" where the the creature attached to The Doctor's then companion Donna Noble in order to change her timeline.
Rex looked into the file of John Forester who had died shortly before the Miracle at the age of 76 and that he was in the cellar when Jack was constantly being killed as seen on Immortal Sins.
As the Miracle took place in 2011 there is no way that Forester could have witnessed Jack being murdered multiple times. Having died at the age of 76 in 2011 this means that he was born in 1935, seven years after Jack's aforementioned murders in 1928.
At the 22-minute mark, Shapiro clearly calls Noah Vickers "Miller."