The Scientific Method is a powerful tool to aid in our understanding of the Universe and how it works.
But.. Does it really have any limitations?
If there currently is a limitation, then it is most likely from a lack (or misunderstanding) of knowledge gathered, the other tools used to gather information, a lack of imagination to conceptualize a new idea, and/or [usually] the failure to follow the Scientific Method (i.e. “Jumping to a Conclusion”).
These would all be flaws on the human side.. not in the methodology itself.