Factual error: When Kirk/Spock enter/leave the Council Chamber, the doors quietly open unaided (as though there were motion detectors in operation), yet the Organian culture - determined by Spock to be approximately Class D minus on Richter Scale of Cultures - would not have had such technology. A fact overlooked by Kirk and more importantly, Spock.
Continuity mistake: When Spock races back into the phaser control room, he places his electronic tablet on the console and kneels to check on the unconscious Styles and Tomlinson. From one shot to the next, the tablet changes its position on the console behind him.
Plot hole: Apparently there is some confusion over the distance between Earth, Starbase 11, and Talos IV. When Spock first meets Pike on Starbase 11 he tells Pike Talos IV is only six days away. Yet when Pike (in the recording) speaks to the Talosians for the first time, he says he is from a star system on the other side of the galaxy. If Talos IV was on one side of the galaxy and Earth was on the other side, it would take hundreds of years at maximum warp to travel from one planet to the other.
Character mistake: Spock tells Kirk that without being able to test their vaccine with the ship's computers, "it could be a beaker of death." The vessel that the vaccine is contained in is a flask, not a beaker. The ship's science officer should know the difference.
Other mistake: On some VHS editions of this episode, the back cover features a picture of what appears to be both good and evil Kirk sitting at a table, however this never happens anywhere in the episode. That picture is actually from the episode "What Are Little Girls Made Of?"