A sect was a subfaction within some religious or political system.
The Kazon were organised into several sects.
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")