The scientific method operates by validating theories through observation and experimentation, if the observations and experimentation is inconsistent with the theory, the theory must be rethought.
As a rough description, sure. I'll assume that the inconsistent results you're referring to are ones that are still inconsistent after all possible sources of error have been ruled out.
This requires that nature is fundamentally materialistic i.e. that everything is reducible to matter, for if it wasn't, their would be nothing to observe and experiment on.
The bolded part above is where the mistake enters your chain of reasoning. Matter is only a small part of the observable universe.
We can also detect anything that has an effect on matter - any measurable effect whatsoever. These things we study in great depth, grouping them into types that we call 'forces'. We can see, study and comprehend a lot more of the universe when we include forces & energy, neither of which are 'matter'.
Because of the hard work of scientists & natural philosophers over the past 300-odd years we now know that everything that affects us in our lives, from the chemical make-up of the food you eat and the air you breathe all the way up to the gigantic nuclear furnace in the sky that brings us heat and light each day, is based on only 4 fundamental forces*! This wasn't an assumption but rather a conclusion reached from hundreds of years of investigation by thousands of dedicated individuals.
The success of science would suggest that this assumption is well founded,
Again, less of an assumption, more of a conclusion. But I interrupt.
... but with science not yet developing a definitive theory of consciousness or reality
... ? ...
Alright, let's start with the second half: We don't need a specific 'Theory of Reality' because Reality is what all of our scientific theories are trying to describe. Our current 'Theory of Reality' would be:
While it may not be definitive (since we obviously don't know everything - if we ever did, science would stop), it's certainly quite comprehensive.
Now back to the first half: Consciousness, or the perception thereof.
We're at an exciting point in our investigations of the universe. We can honestly and confidently state that we've got a pretty good grasp of the fundamentals: we know the basic forces, we know the basic particles.
From these basic concepts we get a lot of emergent behaviour - that is, phenomena that we observe at larger scales that are not apparent at the more minute scale. Physics, chemistry and biology are each very broad areas of study that are built upon or reduce down to each other, and at each level we see emergent properties or behaviours that are not obviously true when zoomed to a different level.
There is no reason (other than hubris) to believe that our consciousness is something other than an emergent property of our biology, and plenty of reasons to suspect that it is. We know that different conscious states can be induced through specific chemicals or physical trauma; we know how hideously complicated a neural net can be; we know that there's no evidence for any new forces that could affect a physical object (such as a ghost/spirit driving your body as some separate thing).
This is not necessarily a bad or scary conclusion, no more so than the discovery that, at the atomic level, solid objects are mostly empty space. We're not going to suddenly sink through the floor, and we're not going to suddenly stop thinking just because consciousness is emergent biology, biology is emergent chemistry and chemistry is emergent physics.
one could wonder if the influence of the assumption of materialism is the reason for the present shortcomings of science.
Your above 'shortcomings' were more ignorance of findings in specific scientific fields and/or a sense of unease brought by contemplation of the conclusions. Neither of which are bad, and neither are they shortcomings of science.
Do you have any actual shortcomings in mind?
So, could the assumption of materialism be a flaw in the scientific method?
Simply speaking, no.
If there are things out there that have absolutely no interaction with matter in any way, shape or form then it is indistinguishable from it not existing. This includes 'other' ways of knowing being invalidated as a means to detect them.** If there is no way to detect or know something, then it is out-of-reach of all human endeavour, not just science.
Theories of spirit/consciousness, 'supernatural' entities, etc. all make the assumption that there's something nebulous out there... and that it can be perceived, manipulated or that this something can have an effect on our lives. Even if we can't pour 'spirit' into a glass, there are still predicted effects are open to scientific investigation!
That consciousness is a fascinating, complex, emergent property of our biology is a conclusion, not an assumption, reached through many years of searching by many dedicated people. This is a triumph, not a shortcoming, of the scientific method.
* These are: Gravity, electromagnetism, the weak nuclear force and the strong nuclear force. If there are other forces at play, they are either infinitesimally weak or operate on infinitesimally short distances.
** We've gotten very good at detecting forces and particles that have nearly zero interaction with matter. For example: Neutrinos have so near to zero interaction with physical matter that trillions can pass through your body every second undetected - and are studied regularly and in detail.