A sect was a subgroup within some religious or political system.
The Kazon were organized into a constantly changing number of sects. At one point in 2371, there were eighteen Kazon sects. (VOY: "Initiations")
One Klingon sect believed the Klingon Empire had lost its way, and went out to search for the kuvah'magh. (VOY: "Prophecy")
Mobar claimed to be part of a religious sect. In reality, he was a con artist. (VOY: "Live Fast and Prosper")
Sects also existed within Bajoran society. For example, the Higa Metar were a sect of the Bajoran Resistance. (DS9: "Babel")