Fox-TV version removes some footage: During the crisis on the Enterprise B, Kirk starts to stand a number of times to offer a suggestion and then thinks better of it, sitting back down. Scotty leans over after this happens a few times and asks if there's something wrong with his chair. Scotty's remark is deleted. After Riker orders the computer to remove the plank, causing Worf to be dumped in the water, his follow-up exchange with Picard is missing - Picard: "Number One, that's 'retract' the plank, not 'remove' the plank." Riker: "Of course, sir. [shouting over the rail] Sorry!"
When Worf explains the workings of 'trilithium', all his words were overdubbed. In the filmed scene (and in the novelization), Worf simply says that trilithium is a very powerful explosive. In the actual film as seen in theaters, Worf's overdubbed lines now say that trilithium is a "nuclear inhibitor" which can stop all nuclear reactions within a star.