Topic: X-Files: Is Scully's skepticism justifiable?

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This is a somewhat random topic, I know, but as I've been re-watching the X-Files (why? I don't know, just decided to re-watch every season), I have become increasingly frustrated with Scully's skepticism to any of Mulder's claims. In season 7 now, and after a few episodes, it's really beginning to bug me. I love Scully as a person, she's kind, warm, funny, smart and guarded in a way that just makes her more likeable. So I kept trying to convince myself that she's just being a good, rational scientist. But is she really? Why are my intuitions telling me she isn't? As such, I set about trying to ground my intuitions to words.

The Good Scientist
Whilst there is some variation in textbooks, it may be generally accepted that there are several key principles to the scientific method:
1) Systematic empiricism: observations organised in a systematic manner
2) Theories must be testable and falsifiable
3) Reproducibility: can be verified independently by others in an objective manner
4) Parsimony: simplest, most natural explanations must be favoured
5) Lack of absolutes or certainty in science
I think my intuitions stem from (5). Scully generally adheres to Inference to the Best explanation (IBE- something a lot of scientists adhere to, not many pseudoscientists). This is best described by Charles Sanders Pierce:
"Facts cannot be explained by a hypothesis more extraordinary than the facts themselves, and among various hypothesis, the least extraordinary must be adopted"
On any single instance of an extraordinary phenomenon, it's perfectly reasonable to adopt a simple hypothesis. If a pig flies into the window of my room on the third floor, it's probably better to assume it was hurled there rather taking on the assumption that it developed the ability to fly after escaping from a secret government facility that was attempting to create a race of super pigs, led by a mad scientist secretly being mind-controlled by a mutant pig named Dave in a plot to overthrow pig farmers everywhere. The problem is, Scully doesn't just face a single instance. Over 7 seasons, she's at least been present to over 140 instances in which the simplest explanation wasn't adequate. Yet she never budges on her skeptical stance, citing it as scientific. But, like many forget, science is not absolute. No good scientist claims to have accessed a universal, necessary truth. Evolution is 99.9% certain, for there are no certainties. Scientists produce models of the world, models that are open to refinement and modification. To therefore be unwilling to accept an alternate possibility despite a large amount of evidence to the contrary is bad science. Good scientists have a healthy amount skepticism but a willingness to change depending on evidence. All scientists are aware of the pessimistic meta-induction from the history of science. Knowledge collapses as often as it accumulates (history provides as with numerous examples of false beliefs we held- e.g aether).As the literary critic Henry Levine so eloquently put it:
"The habit of equating one's age with the apogee of civilization, one's town with the hub of the universe, one's horizons with the limits of human awareness, is paradoxically widespread"

But is she just being rational?

The Rational Scientist
I think Scully's adherence to IBE is mostly an adherence to Induction. Induction is the general idea that, as Hume put it
"Instances of which we have had no experience must resemble those of which we have, and the course of nature continues always uniformly the same"
However, there are philosophical problems with induction. Unlike deduction, an example of good reasoning that guarantees a conclusion, induction offers no guarantee. Just because it may have rained on every Thursday that fell on the 21st of January throughout the history of the world, does not mean it will happen the next time. And, unlike deduction, induction cannot be justified without employing some degree of circularity (the future will resemble the past because the future has always resembled the past). Despite its drawbacks, induction is a form of reasoning employed everyday by some of the greatest minds on Earth, despite its vulnerability to being wrong. This is because induction is a good form of reasoning if and only if it is seen as an instance of IBE (Gilbert Harman, The Inference to The Best Explanation, 1965). Scully seems to faithfully stick to induction, rather than adopting IBE, which would allow someone to adopt a different hypothesis after 140 instances of contradiction. But maybe she is sticking to IBE and I'm misunderstanding. Does this make her Rational?

Miracles
Hume thought that "no testimony was sufficient to establish a miracle, unless the testimony were of such a kind that its falsehood would be more miraculous than the fact it endeavours to establish." No matter how reliable and trustworthy a person is, if they tell you of some miraculous and extraordinary event that contravenes the laws of nature, Hume would admonish you for believing it. He believed there was no reason to believe any testimony of miracles. So, whenever Mulder claims to have seen something extraordinary, Scully is within reason allowed to give his claims no ground. This actually plays out in probability theory too. If you take Scully to be a Bayesian (which she is as she cites statistics fequently), the probability of a miracle occurring is still very low even if you account for testimony from a source of incredible reliability. BUT Bayesianism allows you to adopt a new probability of a miracle occurring if YOU are provided with evidence of the miracle. Now, the show was very careful (to the point of destroying credibility) to make sure that whenever Mulder saw something amazing, Scully was conveniently doing something else so she wasn't exposed to direct evidence, only testimony. But there were enough occasions where Scully saw something extraordinary yet did not adjust her prior probability of the miracle/event occurring to suggest that she wasn't applying the Bayesian concept of probability accurately. She rejected the testimony but ignored evidence. She may seem to come round to the idea towards the end of an episode, only to conveniently forget it an episode later, discarding evidence she had been privy to. Thus, logic cannot be used as an excuse for her skepticism.

tl;dr: I don't think science or logic can be adequately used to defend Scully's skepticism
I'm probably wrong and thinking about this too much