In the jungle when Flynn reads Nicole's (played by Sonya Walger) personality, he says among other things that her father is Argentinian but that she never learned Spanish. Sonya Walger's Father is actually Argentinian however contrary to the film she is fluent in Spanish.
When Flynn and Nicole are walking through the Amazon Jungle, Flynn says something to Nicole, to which she replies "Be still my heart". ER: Be Still My Heart (2000) was the ER episode (season 6 episode 13) where the character played by Noah Wyle (who plays Flynn in the Librarian) is stabbed and almost dies.
The Artifacts in the Library are, Tesla's Death Ray, The Holy Grail, Little Boy(Atomic bomb), The Ark of the Covenant, The Golden Fleece, King Midas, Excalibur, The Goose that laid the golden egg, Pandora's Box, Real Mona Lisa (Copy in Louvre), A Unicorn, Rocketeer's Jetpack, Ali Baba's Flying Carpet, and the Spear Longinus (Spear of Destiny).