[{"createdBy":"","version":[{"isDraft":true},{"isDraft":true},{"isDraft":false}]},{"createdBy":"other","version":[{"isDraft":true},{"isDraft":true},{"isDraft":false}]}]

db.collection.aggregate([{"$match":{"createdBy":"","version.isDraft":true}},{"$set":{"version":{"$filter":{"input":"$version","as":"v","cond":{"$eq":["$$v.isDraft",true]}}}}}])