Even when it was still supposed to have been the pilot episode for the series, Roddenberry and his cowriter, Harold Livingston, had been feuding. His replacement, Dennis Clark (Comes A Horseman) got along even worse with the Great Bird, and Livingston was back in three months. But despite Livingston having it in his new contract that Roddenberry couldn't do any more work on it than he already had, Roddenberry would do rewrites on the sly and then send them to the studio head.
Paramount's original budget was $8 million. The original director and producer were let go once Roddenberry realized just how much the kind of special effects audiences would be expecting after Star Wars and Close Encounters would cost ... that much, and possibly more. Robert Wise was hired as director and the film's budget doubled. He put shooting on hold while he had the sets and (yes) the costumes redesigned. But the cast, already under contract for the now-abandoned sequel series, was still getting paid every week under regularly extended contracts, and finally Paramount said in late summer 1978 that principal photographry had to start.
Wise didn't want to shoot for more than 12 hours a day, resulting in the production getting behind schedule after the first two days.
The feuding between Roddenberry and Livingston continued, at the expense of the script. William Shatner, who titled his chapter on this in Movie Memories "Star Trek: The Emotional Picture", said the cast was getting revisions every two hours. And they hadn't even settled the question of what was going to happen in the third act, until two months had gone by and Leonard Nimoy began mediating between Roddenberry and Livingston at night after shooting.
William Shatner and Leonard Nimoy both requested rewrites during filming to refine the dialogue as they were both unhappy with what had been written for them ("Kirk wouldn't say this"/"Spock wouldn't say that" etc.).
Only after the wrap did Wise check on the special effects, of which he hadn't even seen a demo shot (which concerned him). It soon became apparent that the first special effects house couldn't get the job done so John Dykstra and Douglas Trumbull were hired with only months to go. They had to work around the clock to get the job done.
It was so over budget that Paramount executives were keeping a running tab each day of how much it was such (they had trusted Roddenberry despite the fact that he had never produced a feature film; after this they knew better than to let him again).
According to Wise and Jon Povill, the associate producer, the released film was essentially a rough cut that no one had seen in its entirety before shipping. Wise completed the final cut a day before the premier and had to take it with him to the premiere in Washington. The reels were still wet when they were loaded onto the projector.
What Could Have Been: This film's script was intended to be the pilot episode of Star Trek: Phase II, a Sequel Series to the original show that never materialized. The fact that it was written for a 90-minute (at most) pilot episode explains all the padding in the filmed version.