The active app in the dock has an extra highlight dot on the right for me. In an older version (with a 3.26 shell I think) It behaved correctly. You can also see, that the windowcounter is below the colored dots as well as a little white dot.

Here is the related Issue 776 in Dash-to-Dock
@Whnr,
Why do you say that the dot is extra?
Without the dot, how would you identify which icon represents the app that currently has focus?
(Note, in your image, the Firefox icon is highlighted because you are hovering over it. But if you move your mouse pointer away from it, it will only have dot(s) on the left side, and will look like all the other apps that are currently running).
If nana-4 wants to change this then there must be a different way to visually distinguish the currently focused application from other running applications in the Dock. I see two options:
On a side note, I noticed in your screenshot that the colored dots on the left are superimposed on top of white "running" dots. Do you have the Dash-to-Dock extension, and have you (on the Appearance tab in the settings dialog) selected something other than "Default" for the "Customize windows counter indicators" option? For some reason Materia (and other themes) don't seem to play well with this option. Dash-to-Dock and the Theme BOTH try to draw these dots. The colored dots on the left are from Dash-to-Dock, and the white dots (hidden on the left, visible on the right) are from Materia.
Here is a comparison: The standard GNOME-Shell Theme handles it pretty much as expected. Materia screws it up quite a bit. The only changes were:
there must be a different way to visually distinguish the currently focused application from other running applications in the Dock
Usually you don't seem to see the active app without dash2dock when only showing the activities overview. Dash2dock handles the highlighting very well, as shown below.

So sorry for my late response. I didn't have time to properly investigate this and reply.
I'm placing those white dots assets on the dock just for my aesthetic preferences, because I'm currently not very satisfied with the custom indicators provided by dash-to-dock.
(As @PJSingh5000 suggests,) The best solution for me is to hide the Materia's white dots when using a custom indicator. But sadly, it seems there is no way to do it so far. So I decided to report it to dash-to-dock.
Thanks for your report anyway.
Thankfully, a feature request I filed against dash-to-dock may be accepted and merged. Then we will be able to _hide_ the white dots when using a custom indicator.
The PR #319 will be merged when the new version of dash-to-dock is released (and if the upstream PR is merged).
Good news!