I wish that were the issue, but unfortunately the mods don't appear at all and aren't even viewable in the workbench despite having dozens in my inventory (as well as dozens of weapons). I'm in the process of uninstalling and reinstalling the game right now so hopefully that will fix it.
I have mods available in my inventory, but any time I open a workbench, they do not show up for my weapons. My armor and helmet mods are available and I can modify those without any issue, but can't upgrade my weapons.