Shatner himself probably assumed they had another scene somewhere else in the script. In some cases, he'd inadvertently taken away Sulu's only line in the episode or whatever, but he was probably clueless that this is what he'd done.
I'm not quite on board with that. It's true that actors with a whole script to learn every week can only learn their own parts. But Shatner had a deliberate policy preference that STAR TREK was to be a straight-to-the-point, hero-driven show, not a meandering ensemble piece.
It was always "We tell stories about people," but for Shatner, people meant Kirk and this week's aliens, not the functionaries who take Kirk's orders.
And STAR TREK was cast with that common '60s TV philosophy in mind. The little people were never intended to carry the show. That's why (for instance) Roddenberry could give the recurring female roles exclusively to women he was having sex with. Barrett, Nichols, and Whitney were all putting out for him, and it showed. They were very limited actors.
If TREK had been designed as an ensemble, it would have needed somebody good taking Kirk's orders, an actress with talent and charisma like Marianna Hill. The supporting cast Shatner actually got is precisely what vindicates his hero-driven story preference.