I also have the same problem. As the screenshot of my two external monitors shows, in the Quick Launch and on the vertical (right hand side) monitor, Firefox Nightly appears with its orange icon, while the tray of the left screen shows the blue version.

The Change Icon dialog shows that the icon has no other version, just the orange one. Where does the blue one come from?

After reading the idea from @SidF, I tried to change the scaling of the monitors, which originally were 125% and 100% for the left and right monitor, respectively. I tried every possible combination of 125% and 100%, and some other values too, but the icons always remained, even if I restarted the app between the changes.