Icons for many programs that run in the tray are missing icons.
They end up being just a box with 3 dots.
Is there a way to add icons for specific programs?
I tried the gnome extension Tray Icons: Reloaded which did nothing.
For example one program which is popular Megasync has no icon.
No, not without writing your own shell extension to do so. Apps are supposed to set these icons themselves.
If an app incorrectly sets it's icon, there isn't much you as the user can do.
The problem is Flatpaks. I installed Megasync deb and the icon now appears in the tray.
In that case the maintainer of said flatpak has incorrectly configured it. It is not offically supported by MEGA.