As someone who did a double degree in philosophy and computer science concurrently, I am here to tell you: STEM majors very often
do lack critical thinking skills.
I have watched very smart physics majors struggle mightily (with success, in the end!) in a philosophy of science class because (a) they've implicitly absorbed an extremely naive epistemology, usually some Popperian but simplified thing, (b) they don't have a lot of practice reading and writing prose, and (c) their main coursework has focused on using existing models and methodologies to the near total exclusion of evaluating, analyzing, or comparing them.
Incidentally, that was in a class taught by someone with a graduate degree in STEM himself, who collaborates with working scientists on some of his work as a philosopher— this was an instructor who could very much speak the language of undergrad STEM students.
Critical thinking is also a matter of habit and temperament as much as it is being able to identify (un)sound reasoning itself. If you're not accustomed to seriously examining the structure and functioning of institutions, processes, and social practices, you ain't got it— even if you're extremely sharp with your logical and mathematical intuitions and skills.
That said, widespread innumeracy seems to me much more widely condoned socially than STEMlord parochialism, and is just as detrimental. Especially at an undergraduate level, I think we would benefit from rolling back our increasing specialization a bit. Everyone should have some experience with the work of mathematicians— writing proofs— and everyone should have some engagement with the history-of and philosophy-of some of the STEM disciplines, imo.
This is probably a good time to remind everyone that the empirical sciences are facing an extremely widespread methodological crisis right now¹. I point that out not to say that scientists are stupid or that the problems that add up to the replication crisis are easy to solve, but because critical thinking is exactly what scientists need to do and are doing when they work to address the replication crisis! It's not wrong to push for more emphasis on developing critical thinking skills and habits in science education.
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1: https://en.wikipedia.org/wiki/Replication_crisis