Most liberal arts courses are driven by writing essays where you defend a thesis. The actual validity of your thesis didn't matter so long as you are able to find several points to defend it.
Then you had poor teachers, unless you were taking only courses in the art of persuasive writing (or, as you call it, rhetoric). If your other professors let you get away with this, then shame on them.
As someone who has taught university courses (and who has discussed pedagogy and writing with a lot of faculty in both sciences and humanities), I do see the value in constructing a thesis with supporting evidence as a first step to writing an expository essay. But at some level you do need to question the validity of the argument and the significance of the evidence -- if your professors never required this level of rigor, they did you a disservice.
On the other hand, as someone who has read thousands of student essays over the years, let me also say that faculty are often overwhelmed with simply trying to get students to put together some semblance of a logical chain of an argument in the first place, let alone requiring the rigor you're talking about. That's not to excuse what you describe, but a significant percentage of university-level students have such poor writing skills now that they can get nowhere near the standard you suggest. And professors are often just happy to have a kid submit something that "sounds like an argument," even if it isn't fully rigorous, because it's better than much of the crap that has to be read and graded.
What I commonly saw was students starting with a conclusion and working backwards to find evidence which best fit the chosen thesis. [snip] In a science course this would be called cherry picking the data, in liberal arts, it's called another day.
Well, it's also called "confirmation bias," which is problem both in scientific experimental design and in humanities arguments. Part of the problem is that humanities issues are often not quantifiable in the same way that science ones are, and even if you try to quantify them, you end up with so many interacting variables that statistical analysis can be pretty meaningless. So, in some ways it's related to the fundamental nature of the content of the field -- which still doesn't excuse poor reasoning.
My science course work on the other hand is where critical thinking was encouraged.
Okay, let's see what that entailed....
I was taught how to write logical proofs, I was taught how to represent both everyday situations, and also computational operations in the form of atomic sentences.
That sounds like a course in "formal logic," which is often taught in philosophy departments, not science courses. And as for "represent... everyday situations," I have met many, many science undergraduates who have very little perspective on applying their methods to "real-world problems," unfortunately.
I was taught the dangers of conflating correlation with causation, I was taught the dangers of Type I and Type II errors.
This is basic statistics, which should be a required course for everyone, no matter what major. (Frankly, I think it should be required to graduate high school.)
I was taught about common logical fallacies.
This is traditionally the purview of a rhetoric course in English or the logic courses in the philosophy department, though given your background in Cognitive Systems, I assume you might learn about this in the course of various cognitive biases.
I was taught how to evaluate information critically, I was taught the importance of internal consistency, I was taught how critically examine evidence.
Now we're finally getting to "critical thinking," and this should be important in any rigorous college course, regardless of discipline.
The problem is that those last skills you mention are often much more difficult to apply to real-world scenarios than the earlier "critical thinking" skills you discuss. Formal logic, statistics, etc. are great tools, but the real world is pretty messy. I've met a lot of science majors who simply would have no idea how to approach a vague problem that couldn't be quantified or expressed symbolically -- like "humanistic" problems of ethics or abstract value, etc. Those issues come up in the real world, and the critical thinking required to deal rigorously with them is hard to pull out of raw stats or formal logic.
I'm NOT saying that humanities are the only approach, and I recognize that many humanities courses are badly taught -- resulting in ignorant humanities grads today with bad critical thinking skills. But the problem is not the disciplines themselves, but the rigor we require in those courses. It sounds like your humanities courses did not require that sort of effort, which is unfortunate... but it doesn't mean the whole set of liberal arts disciplines are fundamentally flawed.