main.js

var mongoose = require('mongoose'),
  assert = require('assert')

mongoose.connect('localhost/mydb');

var Schema = mongoose.Schema;

var ContainerSchema = new Schema({
  name: String,
})

var MasterSchema = new Schema({
  name: String,
  container: [{type: Schema.Types.ObjectId, ref: 'Container'}]
});

var PanelSchema = new Schema({
  name: String,
  master: [MasterSchema]
});

var AppSchema = new Schema({
  name: String,
  panel: [PanelSchema]
});

var App = mongoose.model('App', AppSchema);
var Panel = mongoose.model('Panel', PanelSchema);
var Master = mongoose.model('Master', MasterSchema);
var Container = mongoose.model('Container', ContainerSchema);

var container = new Container({name:'page'});
container.save(function(err) {
  var master = new Master({name:'meester'});
  master.container.push(container);
  master.save(function(err) {
    var panel = new Panel({name:'paneel'});
    panel.master.push(master);
      panel.save(function(err) {
      var app = new App({name:'application'});
      app.panel.push(panel);
      app.save(function(err) {
        App.findOne({name:'application'})
        .populate('panel.master.container')
        .exec(function(err, prog) {
          if (err) throw new Error('not found');
          assert.equal(prog.panel[0].name, 'paneel');
          assert.equal(prog.panel[0].master[0].name, 'meester');
          assert.equal(prog.panel[0].master[0].container[0].name, 'page'); // <== fails
          process.exit();
        });
      });
    });
  });
});