Deliberate mistake: To fix the error of the Enterprise firing phasers from the torpedo bay, the Blu-ray version uses footage from "The Best of Both Worlds" to show phasers firing from the dorsal emitter. In doing so, they created a new goof; the planet El Adrel is not visible in the background during these shots.
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Suggested correction: I rewatched the original version on the old DVDs. El Adrel wasn't visible in the original either, so this is not a new error.
Deliberate mistake: When the turtles and April escape the building filling up with water, the shot where the hall is filling up with water is used twice.