The National Center for Complementary and Integrative Health has a concise summary and description of the issues
present day mainstream science and western medicine have with homeopathy:
"Homeopathy is a controversial topic in complementary medicine research. A number of the key concepts of homeopathy are not
consistent with fundamental concepts of chemistry and physics. For example, it is not possible to explain in scientific terms
how a remedy containing little or no active ingredient can have any effect."
[source]
In "potentising" substances, homeopathy 'liberates' matter into 'spirit', into pure vibration/resonance. When a potentised substance - its resonance - is similar to the resonance of the being who is sick - healing, balance ensues. This is called the "Law of Similars" - like cures like. Homeopathy is a Medicine whose essence lies in the world of the immaterial, subtle energies, as is our vital force/ prana / chi... That is why Newtonian based science cannot comprehend how homeopathy can work.
"The unleashed power of the atom has changed everything save our modes of thinking, and we thus drift toward unparallelled catastrophes." (Einstein)The revelation that the universe is not an assembly of physical parts, suggested by Newtonian physics, and instead comes from a holistic entanglement of immaterial energy waves stems from the work of Albert Einstein, Max Planck and Werner Heisenberg, among others.
Quantum physicists discovered that physical atoms are made up of vortices of energy that are constantly spinning and vibrating, each one radiating its own unique energy signature. The atom has no physical structure, we have no physical structure, physical things really don't have any physical structure! Source.