For one, the scientific study of perception itself (not to mention the study of chemistry and physics) brings in to question how much of what we perceive is real. The solid-seeming table not really being at all as solid as it seems, or the small trees in the distance not really being small being some of the commonest and simplest examples. There are plenty of other examples, from optical illusions to a wide variety of phenomena detected through experimental aparatus but not usually available to our senses, such as x-rays, viruses, and so on.
Such phenomena and the stories scientists use to explain them have lead to the widespread questioning of the reality of the world as we commonly experience it, and even to questioning if the world itself is a simulation -- questions from physicists, no less. These are philosophical questions, but ones I'm not convinced that science is equipped to answer. I'm not sure what experiments could ever be performed to determine whether ultimately, deep down, whatever scientific instruments detect or theories postulate is "really real" or just illusion. At the most basic level, it's questionable whether science ever even "gets closer to" some kind of ultimate "truth", or whether they're always just attempts to explain mere apperances.
There are many other objections to the claim that science is the only true, valid, or legitimate way of acquiring knowledge, and to the claim that scientific results are either true or approaching truth. But I'll spare you in the interest of not making this post in to a book or boring you any more than I already have. I'll just point to you these articles on Skepticism[1], Epistemology[2], and Scientism[3] and move on to pointing out that even were we to grant that the practice of science gives us access to truth, there are still some realms off-limits to it, such as (more specifically) ethical questions, and more generally telling us how we should act when given a choice. There are no experiments which can be performed that can show us which is the "right", "moral" or "ethical" choice in any given situation. One could certainly survey some population, but that would only tell you what some people think is right, moral, or ethical, not what actually is (unless you think what the majority believe must be true, which is yet another philosophical position and up for debate). So this is yet another example where science just stands mute, and I don't see any way it'll ever be able to speak on these subjects.
I think most well educated scientists realize these limits of science, and consequently don't make grand claims for the Truth of what they're discovering or the superiority of science over other fields. In fact, those subjects and such claims are off-limits in most if not all scientific journals. It's outside scientific journals, and one could say outside of science proper that such claims are heard, and they're often made either by science fans who are not scientists, or by scientists who really haven't studied the philosophy of science much and get a little too carried away with the popular view of science.
[1] - https://en.wikipedia.org/wiki/Skepticism