Continuity mistake: When Spock shows the others the machine which must be put "in the proximity of the Companion", in the closeup Spock's left arm is up on the machine and we see the chair opposite Spock is empty. However, in the next shot Spock's right arm is up by the machine and Kirk is sitting in that chair. (00:22:10)Super Grover
Plot hole: The crew of the Galileo are stranded because there is a "dampening field" preventing the shuttle craft and its equipment from working. But the device they use to short out the "companion" works.