CursorBatchDeserializationHelper.DeserializeBatch creates a deserialization context that does not support documents with duplicate element names. This prevents the Find() method from being used to query collections with such documents. A fix is to change this line:

var context = BsonDeserializationContext.CreateRoot(reader);

to this line:

var context = BsonDeserializationContext.CreateRoot(reader, b => b.AllowDuplicateElementNames = true);