The following code fails:

var doc = new BsonDocument() { AllowDuplicateNames = true };

doc.Add("a", 1);

doc.Add("a", 2);

var doc2 = doc.DeepClone();

This is because DeepClone does:

{{ BsonDocument clone = new BsonDocument();}}
{{ foreach (BsonElement element in _elements)}}
{{ {}}
  clone.Add(element.DeepClone());
{{ }}}
{{ return clone;}}

Changing the first line to:

BsonDocument clone = new BsonDocument() { AllowDuplicateNames = AllowDuplicateNames };

fixes the problem.