I've read the headline that two things cannot actually touch.
That headline always bothers me. Of course things can actually touch, my fingers are touching the keyboard as I write this.
The real headline is not that things cannot touch, but that everything (including touch) is an interaction between fields. All matter and all interactions are governed by fields at a fundamental level, so that includes contact interactions. In other words, an electron is an excitation of the electron field, so far from not touching you can talk about electrons touching whenever the fields interact appropriately.
In other words, what is the difference when two magnets touch to make a clicking noise and when they push each other away?
Your question is a good question. Since touch is mediated by some fields then why don't we say that two magnets are touching when their magnetic fields are interacting to produce a force? What is special about the fields involved in touching that distinguish them from the magnetic field?
As I said above, there is a specific field for electrons and any electron is an excitation of the electron field (similarly for all other fundamental particles). The electron field and the electromagnetic field are different fields, but they are coupled to each other.
So at a simple level the difference is which fields are overlapping. When magnets touch, they are at such a close distance that their electron fields are overlapping. When they are not so close then their electromagnetic fields are overlapping.
The coupling between the electron field and the electromagnetic field works so that, when the magnets are not touching, the force that they exert on each other changes slowly as the distance changes. However, when the magnets are touching a very small change in distance leads to a very large change in force. This is what distinguishes touching. That sudden change in force is what causes the "clicking" sound that you mentioned.