gistfile1.js

var DM, Document, PM, Property, Schema, assert, async, docs, mongoose;

mongoose = require('mongoose');

Schema = mongoose.Schema;

async = require('async');

assert = require('assert');

mongoose.connect('localhost', 'simple_test');

Document = new Schema({
  name: {
    type: String,
    required: true
  }
});

Property = new Schema({
  data: {
    type: Schema.Types.Mixed,
    required: true,
    "default": {}
  },
  doc: {
    type: Schema.ObjectId,
    required: true,
    index: true,
    ref: 'Document'
  }
});

Property.pre('save', function(next) {
  console.log('pre save', this);
  return next();
});

Property.post('save', function(doc, count) {
  return console.log('post save', doc);
});

DM = mongoose.model('Document', Document);

PM = mongoose.model('Property', Property);

docs = [];

docs.push(new DM({
  name: 'doc1'
}));

docs.push(new DM({
  name: 'doc2'
}));

async.waterfall([
  function(cb_wf) {
    return async.forEach(docs, (function(doc, cb_fe) {
      return doc.save(cb_fe);
    }), cb_wf);
  }, function(cb_wf) {
    var prop;
    console.log("CREATING PROP 1");
    prop = new PM({
      data: {},
      doc: docs[0]._id
    });
    return prop.save(cb_wf);
  }, function(prop, count, cb_wf) {
    return PM.findById(prop._id, cb_wf);
  }, function(prop, cb_wf) {
    assert.deepEqual(prop.data, {}, "got " + (JSON.stringify(prop.data)) + " instead of {}");
    console.log("MODIFYING PROP 1");
    prop.data.my_key = 'my_value';
    prop.markModified('data');
    return prop.save(cb_wf);
  }, function(prop, count, cb_wf) {
    return PM.findById(prop._id, cb_wf);
  }, function(prop, cb_wf) {
    assert.deepEqual(prop.data, {
      my_key: 'my_value'
    }, "got " + (JSON.stringify(prop.data)) + " instead of {my_key: 'my_value'}");
    console.log("CREATING PROP 2");
    prop = new PM({
      data: {},
      doc: docs[1]._id
    });
    return prop.save(cb_wf);
  }, function(prop, count, cb_wf) {
    return PM.findById(prop._id, cb_wf);
  }
], function(err, prop) {
  assert.deepEqual(prop.data, {}, "got " + (JSON.stringify(prop.data)) + " instead of {} for property " + (JSON.stringify(prop.toJSON())));
  return console.log("Done!");
});

Produces:

CREATING PROP 1
pre save { doc: 513e875c010fd2c841000001, _id: 513e875c010fd2c841000003 }
post save { __v: 0,
  doc: 513e875c010fd2c841000001,
  _id: 513e875c010fd2c841000003 }
MODIFYING PROP 1
pre save { doc: 513e875c010fd2c841000001,
  _id: 513e875c010fd2c841000003,
  __v: 0,
  data: { my_key: 'my_value' } }
post save { doc: 513e875c010fd2c841000001,
  _id: 513e875c010fd2c841000003,
  __v: 0,
  data: { my_key: 'my_value' } }
CREATING PROP 2
pre save { doc: 513e875c010fd2c841000002, _id: 513e875c010fd2c841000004 }
post save { __v: 0,
  doc: 513e875c010fd2c841000002,
  _id: 513e875c010fd2c841000004 }

/Users/azylman/Git/node_modules/mongoose/lib/utils.js:413
        throw err;
              ^
AssertionError: got {"my_key":"my_value"} instead of {} for property {"doc":"513e875c010fd2c841000002","_id":"513e875c010fd2c841000004","__v":0,"data":{"my_key":"my_value"}}
    at Promise.<anonymous> (/Users/azylman/Git/test/simple_test_case_maybe.js:94:10)
    at Promise.addBack (/Users/azylman/Git/node_modules/mongoose/lib/promise.js:128:8)
    at Promise.EventEmitter.emit (events.js:96:17)
    at Promise.emit (/Users/azylman/Git/node_modules/mongoose/lib/promise.js:66:38)
    at Promise.complete (/Users/azylman/Git/node_modules/mongoose/lib/promise.js:77:20)
    at Query.findOne (/Users/azylman/Git/node_modules/mongoose/lib/query.js:1533:15)
    at model.Document.init (/Users/azylman/Git/node_modules/mongoose/lib/document.js:229:11)
    at model.init (/Users/azylman/Git/node_modules/mongoose/lib/model.js:192:36)
    at Query.findOne (/Users/azylman/Git/node_modules/mongoose/lib/query.js:1531:12)
    at exports.tick (/Users/azylman/Git/node_modules/mongoose/lib/utils.js:408:16)

As you can see, the second property is stored in to mongo correctly according to its pre and post save handlers, but findById adds the same data property that we saved to the first property.