Despite being Celtic in origin, the runes on the game, statute, and stone in the beginning are Nordic.
USS Blueback (SS-581), the decommissioned Barbel-class submarine, is in fact not located in Boston but in possession of the Oregon Museum of Science and Industry, which has at least partially been used as the museum set for this episode.
There are no hinges on a sarcophagus.
In this episode of the Librarians, toward the end where all the librarians are standing in unity before Apep the god of chaos, if you listen carefully to the music and the words that Flynn is speaking you will notice distinct similarities between that scene and the last part of Doctor Who (2005), The Eleventh Hour (2010) where Matt Smith appears before the Atraxi as the new Doctor. The background music is--or bears a very strong resemblance to--the piece titled "I Am the Doctor."
The Boston Museum of Science logo is not actually a red butterfly on a white background, it's a white planet in orbit on a red background.