Database
[{"_id":NumberLong(2761632),"data":{"field.with.dots":{}}},{"_id":NumberLong(2761633),"data":{"field":{with:{dots:{}}}}}]
Query
db.collection.aggregate([{$addFields:{dataKv:{$filter:{input:{$objectToArray:"$data"},cond:{$ne:[{$indexOfBytes:["$$this.k","."]},-1]}}}}},{$match:{$expr:{$ne:[{$size:"$dataKv"},0]}}},{$project:{dataKv:-1}}])