isinstance(doc, collections.Mapping) == False

--> 209         return {'syllabus': self.schema.dump(syllabus).data}

ipdb> s
--Call--
> /Users/Vic/projects/brain2/venv/lib/python3.6/site-packages/marshmallow/schema.py(458)dump()
    457
--> 458     def dump(self, obj, many=None, update_fields=True, **kwargs):
    459         """Serialize an object to native Python data types according to this

ipdb> n
> /Users/Vic/projects/brain2/venv/lib/python3.6/site-packages/marshmallow/schema.py(473)dump()
    472         """
--> 473         errors = {}
    474         many = self.many if many is None else bool(many)

ipdb>
> /Users/Vic/projects/brain2/venv/lib/python3.6/site-packages/marshmallow/schema.py(474)dump()
    473         errors = {}
--> 474         many = self.many if many is None else bool(many)
    475         if not many and utils.is_collection(obj) and not utils.is_keyed_tuple(obj):

ipdb>
> /Users/Vic/projects/brain2/venv/lib/python3.6/site-packages/marshmallow/schema.py(475)dump()
    474         many = self.many if many is None else bool(many)
--> 475         if not many and utils.is_collection(obj) and not utils.is_keyed_tuple(obj):
    476             warnings.warn('Implicit collection handling is deprecated. Set '

ipdb> s
--Call--
> /Users/Vic/projects/brain2/venv/lib/python3.6/site-packages/marshmallow/utils.py(63)is_collection()
     62
---> 63 def is_collection(obj):
     64     """Return True if ``obj`` is a collection type, e.g list, tuple, queryset."""

ipdb> n
> /Users/Vic/projects/brain2/venv/lib/python3.6/site-packages/marshmallow/utils.py(65)is_collection()
     64     """Return True if ``obj`` is a collection type, e.g list, tuple, queryset."""
---> 65     return is_iterable_but_not_string(obj) and not isinstance(obj, collections.Mapping)
     66

ipdb> s
--Call--
> /Users/Vic/projects/brain2/venv/lib/python3.6/site-packages/marshmallow/utils.py(51)is_iterable_but_not_string()
     50
---> 51 def is_iterable_but_not_string(obj):
     52     """Return True if ``obj`` is an iterable object that isn't a string."""

ipdb> n
> /Users/Vic/projects/brain2/venv/lib/python3.6/site-packages/marshmallow/utils.py(54)is_iterable_but_not_string()
     53     return (
---> 54         (isinstance(obj, collections.Iterable) and not hasattr(obj, "strip")) or is_generator(obj)
     55     )

ipdb> obj
Syllabus(id='596b04c9b0207a542963af87', title='First Syllabus', ...)
ipdb> isinstance(obj, collections.Iterable)
True
ipdb> isinstance(obj, collections.Mapping)
False
ipdb>

MongoeEngine documents support dict interface
https://github.com/MongoEngine/mongoengine/blob/a7cab513695ba1814d9316719429d63249fb97dc/mongoengine/base/document.py#L215
mongoengine==0.11.0
But still isinstance(obj, collections.Mapping) == False. This causes MarshMallow to think it's a sequence.

    475         if not many and utils.is_collection(obj) and not utils.is_keyed_tuple(obj):
--> 476             warnings.warn('Implicit collection handling is deprecated. Set '
    477                             'many=True to serialize a collection.',
    478                             category=DeprecationWarning)

Start with marshmallow/utils.py:is_collection and MongoEngine's mongoengine/base/document.py around line 215; reproduce Schema.dump on a MongoEngine document and inspect the Mapping and iterable checks shown in the report. Done means the document is no longer treated as a sequence during dump, with a regression test covering this behavior.