[{id:123,contactsOfAppUsers:[{id:"abc",contactsArray:["9999911111","9999922222"]},{id:"efg",contactsArray:["9999933333","9999944444"]},{id:"hij",contactsArray:["9999955555","9999933333"]}]}]

db.collection.aggregate([{$project:{_id:0,matchingObjects:{$filter:{input:"$contactsOfAppUsers",as:"numbers",cond:{$in:["9999933333","$$numbers.contactsArray"]}}}}},{$addFields:{matchingObjects:{$map:{input:"$matchingObjects",as:"matchingObjects",in:{phoneNumbers:"$$matchingObjects.contactsArray",id:"$$matchingObjects.id"}}}}}])