I think it is because the links don’t always match the name of the note being linked.
What markdown output would you like to see in that case? Replace the text inside the square brackets with the name of the target note so that the link will work?
if you were to do it in python, which packages would you use?
I’d have to dive into xml processing in python to give you a sensible answer. If helpful I could create a toy example?
If using actions to link files you need to additionally careful of some characters being used in note titles, or paths to them: see more. In such contexts, I’d name very defensively and avoid non-alpha-numeric characters.
That would be really interesting for me as I am slowly learning Python 
Very kind of you to offer.
It occurred to me that ideally it would just ignore these instances and leave the text as it is, without the link. Or it could embrace the text with square brackets and add the note name in between parenthesis. E.g. [some text](actual note name). This actually works in some markdown apps. (But I am not really sure this is what caused the error in the first place).