db={"articles":[{ref_id:ObjectId("5ebadde78da8f3de641064a5")},{"ref_id":ObjectId("5ebaddec8da8f3de641064b7")},{"ref_id":ObjectId("5ebaddec8da8f3de641064c9")}],"another_collection":[{"_id":"5eb25d1fe519051af2eeb72d"},{"_id":"5ebaddec8da8f3de641064b7"},{"_id":"5ebaddec8da8f3de641064c9"},{"_id":"5a934e000102030405000003"},{"_id":"5a934e000102030405000005"}]}

db.articles.aggregate([{"$group":{"_id":"1","ids":{"$push":{"$toString":"$ref_id"}}}},{$lookup:{from:"another_collection",localField:"ids",foreignField:"_id",as:"tmp"}},{"$project":{total:{$size:{$filter:{input:"$ids",cond:{$not:{$in:["$$this","$tmp._id"]}}}}}}}])