[{flags:[{featureFlagId:"1",name:"flagName"},{featureFlagId:"2",name:"flagName"},{featureFlagId:"3",name:"flagName"}]}]

db.collection.find({$and:[{flags:{$elemMatch:{featureFlagId:"1",name:"flagName"}}},{flags:{$elemMatch:{featureFlagId:"2",name:"flagName"}}}]})