"Set" has a world of meanings, and
all of them are a little fuzzy. In most of its verb meanings, "set" means
(roughly) "place" or some variation. E.g., Set (place) the box down, set
the hen to the eggs, set (adjust) the thermostat. In noun forms, however,
"set" frequently means an assembly of items--such as chess set, television
set. These senses seem unrelated, and it turns out that that's exactly
right. Set (to place) is from OE settan (IE *sed-), which
was a form of "sit." Set (a group) is from OF<L secta (same word
as SECT, a group of believers), meaning group. In English, the two words
have been somewhat confused, so that "set" (group) has come to have the
sense of a group set together.
"Sect" (group) has been even more confused. The word started off (in L.) just meaning a group united by common interest, from (L.) sequi "follow". (Compare "sequel.") But it was a homonym to a word meaning divide (compare "bisect," "dissect," "section"). This similarity (confusion) has caused "sect" to take on the idea of separation or division. So, a sect is now (usually) a part of a larger group, distinguished by some different belief or practice.