Database
[{_id:ObjectId("669fdc567085fd4c423449b9"),internalProp:[ObjectId("669fdc567085fd4c423449b9"),ObjectId("6661ebe9a857d3b793b47f3d")]},{_id:ObjectId("669fdc567085fd4c423449ba")},{_id:ObjectId("669fdc567085fd4c423449bb"),internalProp:[]},{_id:ObjectId("669fdc567085fd4c423449bc"),internalProp:[ObjectId("669fdc567085fd4c423449b9"),ObjectId("6661ebe9a857d3b793b47f3d")]}]
Query
db.collection.find({"$expr":{"$and":[{"$ne":[{"$ifNull":["$internalProp",[]]},[]]},{"$not":{"$in":["$_id","$internalProp"]}}]}})