how to change the icon theme in dock and applications menu without changing the indicator icons and Pantheon icons?

Switch icons back to default. In usr/share/icons/numix-circle. Open up your index.theme file with text editor A few lines down there will be a line saying

Inherits=numix

Change it to say

Inherits=elementary,gnome,hi-color 

In the tweaks panel, select Numix Circle now numix theme will apply to both plank and sligshot menu only. indicator and pantheon icons will stay as default. (this solution was given by Adderbox76 in reddit )