The main thing to note is that when electromagnetic waves propagate in some medium other than vacuum, then the medium itself may be driven by the electromagnetic waves into some wave-like oscillation. For materials such as glass and water this is what happens. The consequence is that although we say in everyday language that "light" is propagating through the glass, or "light" is propagating through the water, the situation in full is not quite as simple as that. Really a wave of polarization of the material is propagating along with a wave of disturbance of the electromagnetic field. The overall result is a wave whose speed can be less than the maximum speed of causality. It is ok in everyday language to refer to this wave as "light" but in more careful physical analysis it would be called a "wave of electromagnetic field and material polarization".
The causal phenomena going amongst all the atoms or molecules are still going at the maximum speed, and in such a way as to keep everything in step in this wave of electromagnetic field and material polarization.
You can also have other things moving through the medium at faster than the speed $c/n$ (where the refractive index $n > 1$), but slower than $c$. For example: electrons, protons, neutrons, neutrinos, or anything in principle (if it does not disturb the medium too much). Also if $n \simeq 1.5$ is the refractive index at optical frequencies, you can still have electromagnetic waves of some other frequency (e.g. gamma rays) propagating at $c$ in the medium.