During the scene where the Coon interacts with Cthulhu, the pair was seen heading for San Francisco, which was already destroyed in the episode Smug Alert from Season 10.
While on Clyde's computer, the article on '10 Cultists arrested' was shown in a Microsoft Windows program, but above it there is a taskbar used only in Apple Inc. computers.
During the scene where the Coon and Friends were selling lemon bars, the first customer said he'll buy 20 bars when he only took 3 bundles, which is a total of 15 lemon bars. Note that each bundle contains 5 of such bars.
Before the last customer arrived at the stall, there are 3 bundles left. But at the next shot, only 2 bundles are seen.
Kenny (as Mysterion) briefly spoke in his normal, un-muffled voice upon seeing the picture of his parents being arrested, making this episode the 3rd (excluding the movie) that he had done so, the last one being Season 11's Lice Capades.
Full list of Coon and Friends' secret identities:
Cartman - The Coon
Kyle - The Human Kite
Stan - Toolshed
Kenny - Mysterion
Clyde - Mosquito
Token - Tupperware
Timmy - Iron Maiden
Bradley - Mintberry Crunch
It is revealed in this episode that Kenny's mother, Carol McCormick now has a job as a dishwasher in the Olive Garden.
The famous catchphrases after Kenny dies hasn't been used without any alteration since Season 10's Make Love, Not Warcraft, and the first since Season 8's The Jeffersons following a real Kenny death.
The two Star Trek geeks from Season 4's 4th Grade, the four Goth Kids from Season 7's Raisins, Nelson, Randy's work friend from Make Love, Not Warcraft and Mr. Adler make a comeback to South Park, only to be members of the Cthulhu cult.
My Neighbor Totoro: Cartman interacting with Cthulhu while on his belly as well as the song playing while flying with Cthulhu is a reference to the film My Neighbor Totoro