All Document object properties are persisted regardless of mapping instructions.

class Users_Model_User
{
    public $id;
    public $username;
    public $password;
    public $myRuntimeProperty = 'some value';
}

Users_Model_User:
db: my_db
collection: users
fields:
    id:
        fieldName: id
        id: true
    username:
        fieldName: username
        type: string
    password:
        fieldName: password
        type: string

$user = new Users_Model_User;
$user->username = 'hello';
$user->password = 'world';
$this->dm->persist($user);
$this->dm->flush();

The result is "myRuntimeProperty" is saved to the db.
This causes problems for several properties such as "_propertyChangedListeners" which, once saved and later loaded back from the database, overrides the array of object listeners with a string of "Array"

If this is not a bug:
I have search everywhere for an answer. All the docs, mailing list, irc, blogs. If this is not a bug the solution needs to be better documented.

Temporary fix:
Use Docblock Annotations, set the unwanted properties with @NotSaved
(Unless there is also a way to set NotSaved using YAML?)