I cannot count how many times CSV "format" has caused problems for me..
In my country the decimal separator is comma, instead of punctuation.
This causes problems when importing and exporting with this "format".
Just few weeks ago I had fun times working with API returning CSV in unknown encoding. Hopefully they will never make changes (you cannot always trust headers). Ah and i do love when CSV is missing headers and someone adds data into middle.
Of course some of these issues can be avoided by doing the things "right". Sadly you cannot trust this in real life. People write ugly structures in JSON, but at least you can validate results..
While there are issues within Python side, I think it is quite unfair to use numpy as an example.
My reasoning is that the numpy project is meant for scientific and prototyping purposes, but many times people are using it as an shortcut and include the whole thing into their project.
That being said, the quality in these packages does vary depending on who developed them. But I think this is a problem that exists with all languages where publishing packages is relatively straightforward.