There are many possible critiques of scientific method, from many different viewpoints and for many different reasons. Many of these are fairly technical, or rightfully should be, such as the application of the Heisenberg uncertainity principle, a rather technical law about the impossibility of measuring electrons, into a general statement about the role of the observer in defining the observed. Some critiques of science are based on the obvious history of science as being clearly biased by social prejudices, such as the infamous "nine out of ten doctors prefer camels" or the "science" of eugenics. Many critiques of science don't even attempt to have any kind of logical or conceptual basis, but instead appeal to people's preference that it should be the nature spirit, and not photosynthesis, that makes the plants grow.
One of the best critiques of science, however, was one I learned from reading Matrin Heidegger's book What is a Thing. I am not a trained philosopher, so my interpretation of what exactly Heidegger was trying to say may not be in accordance with the general interpretation of his views. This is, however, what Heidegger's words inspired me to think:
Heidegger points out that in the famous Tower of Pisa experiment undertaken by Galileo Galilei, to prove that objects of different sizes would fall at the same speed, the objects did not actually hit at the same time, and that was clear to everyone present (I don't know exactly what source Heidegger uses for it), but that the only after factoring in air resistance and the like were the bodies falling at the same rate. In other words, Gallielo was imagining the balls dropping in a vacuum, and not only in a normal vacuum, but in the most perfect vacuum ever, mathematical space, the Cartesian grid. Heidegger then points out that the major advance that led to modern science was not observation, but rather mathematical projection. In other words, scientists were able to undertake experiements because they imagined a neutral world space in which experiments would be unaffected by outside factor. In other words, the view of science is of particles moving around in a field with homogenous properties.
This then, is Heidegger's thinking. My own thinking goes a few steps farther. Perhaps because I am familiar with the Journey to the West, I know of the traditional Chinese system of metaphyisics, the Tai ji, the yin and yang, the five phases and the ten thousand things. It is a rather myriad form of metaphysics, perfect to hang a tragic love story or swashbuckling crazy monkey story off of. However, it is perhaps not best suited for high precision laboratory work. However, although this complicated metaphysical belief system is no longer used, science is still based on a metaphysical system. In the modern scientific belief system, there is space and matter. Matter moves around in space and changes form in space, but it can not actually affect space. It is quite impossible it seems, to change the gravitational constant or the 10 trillionth digit of pi by lighting a match, or even by a star going super nova.
From this observation that there seems to be unchanging laws of the universe, it is easy to deduce that the laws of the universe are an independent principle, out there whatever is going on in them. Since every billiard ball we ever drop will follow these laws, it is easy to deduce that the laws are independent of what is going on inside of them. We could stretch this to say that if a billiard ball "appeared out of nowhere", as it were, it would still follow the laws of physics, because these laws are independent of what takes part in them.
However, this two principle of metaphysics may be just as useless as the ornate monkey and his travelling companions metaphysics. Why does the monkey even need one friend? Because, the truth is, there is no "out there" for a billiard ball to suddenly appear out of and thusly follow the laws of physics.
The belief that there is an independent "laws of physics" that we can depend on no matter what arrangement the particles inside of it start out in is based on the fact, or the belief that we can somehow rearrange situation inside the universe. Which, of course, to our everyday experience we can (it may be time for me to move my desk out of this corner soon, after all), but within the bounds of the entire system of physics, nothing can be cut and pasted from one location to another. This is the philosophy of superdeterminism, which states that things can not be "explained" by "physical laws", because we can never remove things from those laws. The things and the laws are one.
Thus, we see that the scientific viewpoint, which simplified the old complicated "four humours", "seven spheres" cosmology down into atoms and the void can be reduced down even futher into "stuff just happens, there is no way to investigate the cause".