You're right, reproducibility is a problem in science, all science and not just ML (again, as you say), so I don't think that proves anything wrong with Python.
That is true, but maybe Python doesn’t help with its primarily interpreter-based ecosystem (think of jupyter) where a result may only worked for the author because a variable he/she uses used to refer to something else no longer there in the source code (but still defined). Which bit me more than once with for example sage - but it may be simply a problem with jupyter/the way the scientific community writes code.