After Berg/Harberts were fired, there was a production hiatus of a few weeks (I believe following shooting of The Sound of Thunder). Some reshoots were announced right around that time as well. At that point the season took a wide veer, with all of the pseudo-religious mystery vanishing, and the Control plot coming to the fore. Also, originally they claimed that Spock would never appear as an adult in Season 2, and then he ends up a big character in the later half. Peck had a voice log in Brother, but some people believe it was overdubbed - that originally the scene was supposed to have just visuals.