In the video game, when the wolves are chasing down the player Frodo Baggins, they hesitate as Frodo continues to run away from them. The wolves wouldn't stop and hesitate as they would bravely pounce upon their prey and Frodo would've still had to attack them with his stick.
When Gandalf tells Frodo to give him the One Ring to throw in the fireplace, he actually touches the One Ring before throwing it in the fireplace. This would've corrupted Gandalf if he touched it, in the book, he wouldn't even touch it with his bare hands. But when Frodo offers the ring to Gandalf, he immediately says no even though he accidentally touched it.
When the "Lord of the Rings: The Fellowship of the Ring" for Playstation 2, Xbox ends on a cliffhanger. The fate of Boromir at Amon Hen is unknown but he likely died from Uruk-hai shooting arrows into him and the Uruk-hai army captured Merry and Pippin which is missing from the video game. Also missing for "The Two Towers" sequel is Frodos long journey with Sam and their guide Gollum on the quest to destroy the one ring on Mount Doom, climbing the cliffs, going through the marshlands, their meeting with Faramir, Frodo getting wounded by Shelob the giant Spider in Cirith Ungol and Sam Battling it and defeating it but Frodo gets captured by orcs and taken away. Also the journey involving Aragorn, Gimli, Legolas traveling to Rohan on foot and meeting Gandalf the White is missing as well as the war against Sarumans Uruk Hai army at the fort of Helms Deep. Merry and Pippins journey in Fangorn Forest with Treebeard and the Ents and the invasion of Isengard. Saruman and Wormtongue being expelled from Isengard has never been shown in the game.
Also missing for the second sequel "The Return of the King" is Saurons huge army invading Minas Tirith, the Witch King being killed by a woman warrior Éowyn and a Hobbit named Merry and being defeated and the final showdown with Gondor army gathering at the Mordor gates to challenge and distract Sauron and face his orc army. Meanwhile at Mount Doom, Sam rescues Frodo from the orcs stronghold their final journey in the land of Mordor, the climb up Mount Doom but Frodo resists throwing the ring in the lava pit, puts on the one ring and turns invisible, then Gollum attacks Frodo and they wrestle each other for the one ring inside Mount Doom, Gollum bites off Frodos finger for the one ring and then Gollum falls into the lava pit with the one ring, defeating Sauron for good. Which is missing and has never been shown in the game.
Finally missing from the game is "The Scouring of the Shire" which has been hinted in the Playstation 2 and Xbox game, in the Mirror of Galadriel scene in which Sam looks into the water, he is upset by the vision of the Shire being taken over by Ted Sandyman, the Ruffians and his Gaffer being kicked out of his home. Lotho and Lobelia Sackville-Baggins has made money on Pipeweed sales to Saruman, Lotho took over the Shire ordered the Shire to be industrialized in which the Ruffians including Ted Sandyman cut down the trees, dug up Bag End road and built a brick factory to replace the old Windmill. Later on, the Hobbits were made slaves or imprisoned including Lobelia who stood up against the ruffians. After Saruman and Wormtongue were expelled from Isengard, they went to the Shire and Wormtongue murdered Lotho and took over Hobbiton, Saruman was nicknamed Sharkey. Frodo, Sam, Merry, Pippin head home to the Shire after successfully destroying the one ring only to find the Shire in ruins and taken over by Ruffian men. They meet with Farmer Cotton and the Hobbits and they battle for the Shire at The Battle of Bywater in which they kill over 100 Ruffians, they have a showdown with Saruman but Wormtongue kills Saruman with the knife and Wormtongue gets shot by arrows and dies. Frodo and the hobbits clean up the Shire they rescue Lobeila who gives them back their home before she dies and Sam plants a new seed in the Shire, he marries Rose and has children. But Frodo leaves for the Grey Havens on a ship for the tortured wounds he endured while carrying the one ring. Which is missing and has never been shown in the game.