The radioactive waste in the Candy Kingdom most likely originated from the Mushroom War.
The tree Shoko dies under later grows into the tree that the treehouse is built upon, her body perhaps acting as a fertilizer to make it grow as big as it is in the present.
The game installed on BMO, that hypnotizes Finn is identical to the real life game “Super Hexagon”.
The game (entitled “regression simulator”) that Jake loads on BMO to trigger the Vault opening looks very similar to the indie game Super Hexagon.
The “regression simulator” is similar to “Assassin’s Creed,” in which the main character experiences many of his ancestor’s lives.
In the scene where Princess Bubblegum talking to Shoko, Princess Bubblegum said “Amen” which is a phrase used as an affirmation to a strong agreement and also it is a phrase used to end Christian prayers.
The outfit Princess Bubblegum wore is similar to outfits the Japanese wore in their farming era. “Shoko” is a Japanese name.
The episode title refers to “The Creeps,” when Finn first experiences the “Ghost Lady" and places his memory of the incident in "The Vault" of his mind.