I followed the steps in https://forums.ghostbsd.org/viewtopic.php?f=54&t=1921 to update to FreeBSD 13.
Everything is working properly, but I'm missing some icons.

In the Applications menu, I am missing the icon for the "Sound and Video" item and Rhythmbox.
In Software Station, I'm missing the icon for the "All Software" button.
I have Remmina installed, and that is missing most of it's icons.

I reinstalled Remmina and the GhostBSD-mate-themes and GhostBSD-mate-settings and GhostBSD-icons, but the icons are still missing.

Is there a different package that I can reinstall to get these icons back?

you could probably try to reinstall hicolor-icon-theme mate-icon-theme and adwaita-icon-theme.

I encountered a similar problem after the update. I was able to fix it by reinstalling gdk-pixbuf2 and libXrandr, and then rebooting.

If the problem persists, the error log in "~/.xsession-errors" might contain some useful information.