I have since come across a solution and will share it here in case any future people have this issue.

If you are running Wayland, then you can add this line to Factorio's Steam Launch Options

SDL_VIDEODRIVER=wayland %command%

This will force Factorio to run with its native Wayland support, thus ...

Sorry for the necropost but I ran into this again and figured it might help someone.

It seems to be an issue on systems that run Wayland while Factorio is set to prefer X11, since the interop with the clipboard is fairly cursed. If using the X11 bridge under Wayland, you can work around it by ...