Don't other languages cause issues as well? If you wrote your python code in 2.7, it probably won't run in 3.6 without some modifications. Although, with Python everything is free and you can work anywhere without your boss needing to buy a license.
The main point is auditability. Closed source libraries can have errors that can't be audited by the scientific community.
That I would agree with. I probably won't peek under the hood and fix any bugs with numpy, but someone else probably will.
Kip Thorne (pretty famous physicist) uses Mathematica for his work almost exclusively if i understand an interview they did with him correctly.