There are a number of reasons.
However, the most important is that the method of scientific investigation is vastly different than belief in spirits. There’s no real “methodology” when it comes to belief in spirits. It’s whatever seems intuitivelycorrect. In this sense, there’s absolutely zero intellectual humility involved.
Contrast this with the scientific method that takes into account human fallibility and attempts to place safeguards that will help us from fooling ourselves.
This is a massive difference in epistemic “first principles” if you will. Belief in spirits assumes that your senses and your interpretation of those sensory inputs are flawless. The scientific method assumes the opposite: That you are the easiest person for you to fool.
Notice that I keep saying “scientific method” and not “science”. This is for a reason: When people talk about belief in science in contrast to belief in some other “way of knowing”, they are attempting to compare dogmas, or lists of facts. If you think the most important thing about science is that it’s a list of facts that you have to believe or you’re “wrong” then you’re already starting on the wrong foot.
The power of science lies in its methodology. The only reason any list of facts that come from the scientific method have any relevance in the first place is because of the methodology. The methodology is all about inching closer to what’s actually real, and as we inch closer and closer those “lists of facts” may change. It’s all about constant refinement and improvement, the hallmark of any endeavor that has any worth. No such methodology exists for belief in spirits.
Distilled to its most basic form, the scientific method is a system of logic applied to uncertainty. Or in other words, probability theory. Other systems of logic that operate under uncertainty, if they want to get at what’s most likely correct, properly utilize probability theory. This applies to science, medicine, law, history, military intelligence, and many other fields that are serious about getting the best footing possible in a sea of uncertainty.
Belief in spirits follows no models of probability. And in many cases, actively fights against having cold, impersonal logic and probability applied; any field that has a negative view of logic and probability is an anti-epistemology.
And is worthless as knowledge.
That is the main difference between the scientific method and belief in spirits. One is actually a rigorous, self-improving, and self-critical system. The other actively tries to obscure any acquisition of knowledge.
 Belief in God Boils Down to a Gut Feeling
 Amazon.com: Probability Theory: The Logic of Science (9780521592710): E. T. Jaynes, G. Larry Bretthorst: Books
 Probability and uncertainty in clinical and forensic medicine
 Probability—The Logic of the Law | Oxford Journal of Legal Studies | Oxford Academic
 Aviezer Tucker . Our Knowledge of the Past: A Philosophy of Historiography . New York: Cambridge University Press. 2004. Pp. 291. $70.00 | The American Historical Review | Oxford Academic
 Can Subjective Probability Be Expressed As A Number? What Does The CIA Say?