[{"user":"60e5f88159292f575c0ca17f","questions":[{question:"aaaaaaa",id:"1"},{question:"bbbbbbb",id:"2"},{question:"ccccccc",id:"3"}]}]

db.collection.aggregate([{"$unwind":"$questions"},{$match:{"questions.id":{$in:["1","3"]}}},{$group:{_id:"$_id",questions:{$push:"$questions"},user:{$first:"$user"}}}])