Database

[{"members":["userIdOne"]},{"members":["userIdTwo"]},{"members":["userIdOne","userIdTwo"]},{"members":["userIdOne","userIdTwo","userIdThere"]}]

Query

db.collection.aggregate([{$match:{$expr:{$eq:[{$setEquals:["$members",["userIdOne","userIdTwo"]]},true]}}},{$count:"count"}])

Result