[{"_id":ObjectId("4e8ae86d08101908e1000001"),"a":{"a_1":11,"a_2":22},"b":{"b_1":111,"b_2":222},"c":{"c_1":1,"c_2":2},"anomalies":["a","b"]},{"_id":ObjectId("4e8ae86d08101908e1000002"),"a":{"a_1":11,"a_2":22},"d":{"d_1":222,"d_2":333},"e":{"e_1":1,"e_2":2},"anomalies":["a","d"]}]

db.collection.aggregate([{$replaceRoot:{newRoot:{$mergeObjects:[{_id:"$_id"},{$arrayToObject:{$filter:{input:{$objectToArray:"$$ROOT"},cond:{$in:["$$this.k","$anomalies"]}}}}]}}}])