[{"_id":ObjectId("5e82661d164941779c2380ca"),"name":"something","values":[{"id":1,"val":"x"},{"id":1,"val":"x"},{"id":2,"val":"y"},{"id":1,"val":"xxxxxx"}]}]

db.collection.aggregate([{$unwind:"$values"},{$group:{_id:"$values.id",values:{$first:"$values"},id:{$first:"$_id"},name:{$first:"$name"}}},{$group:{_id:"$id",name:{$first:"$name"},values:{$push:"$values"}}}])