It failed to explain how atoms of different elements differ from each other i.e. It did not tell anything about the structure of the atom.
It could not explain how and why atoms different elements combine with each other to form compound atoms or molecules.
It failed to explain the nature of forces that bind together different atoms in a molecule.
It failed to explain Gay Lussac's law of combining volumes.
It did not make any distinction between ultimate particle of an element that takes part in reactions (atoms) and an ultimate particle that has independent existence (molecule).