Now, that's something you don't do when you write a new section by yourself but that might happen if you're using templates. Even if autosigning templates (currently) don't work, this issue should be fixed:
If the title field is left blank but an edit summary was entered, the edit summary is taken as the title and the standard summary /* $1 */ New section is used.
This is caused by the very old idea of just moving the edit summary texbox above the edit textbox when a new section is added instead of using a seperate title textbox. The API works accordingly.
My suggested solution is (sorry that this requires a breaking API change but I think not many bots actually use this API feature) that the edit summary will not automatically be used as the title. Instead, if just a title and not an edit summary is given, the summary will be autofilled. If an edit summary is unwanted (whyever), an empty edit summary parameter can be added to the api request