[{"key":1,a:[{p:[{id:4},{id:6}]}]},{"key":2,a:[{p:[{id:2},{id:3},{id:3}]}]}]

db.collection.aggregate([{$unwind:"$a"},{$unwind:"$a.p"},{$group:{_id:"$a.p.id",cnt:{$sum:1}}},{$match:{cnt:{$gt:1}}}])