As was the case for nearly every other scripted show on the air at the time, Star Trek did a mixture of new episodes and repeats of previously-shown episodes.
Just do the math: if 26 new episodes are produced for a season, yet the season schedule calls for anywhere from 35-45 weeks of programming in the show's assigned timeslot, you're going to have to fill those other dates in the schedule with reruns.
Usually, there would be several weeks of all-new episodes, followed by a couple of weeks of repeats, then more new eps, a couple of repeats, etc. Reruns tended to fall during weeks when widely-celebrated holidays or major events meant viewers might be less likely to watch anyway.