wl-clipboard will work on GNOME/Mutter, but note that due to the security design of Wayland, it can’t always work very well. The trouble is that in Wayland, usually only the focused surface can access or manipulate the clipboard, and nominally CLI programs don’t have a surface to begin with. On wlroots-based compositors, this can be mitigated using the wlr-data-control protocol, but GNOME doesn’t support that, so wl-clipboard needs another hack to work. If it is unable to steal focus briefly, e.g. because an always-on-top window is being displayed, it may not work as intended.
Are you using a terminal that is “always on top”, like a dropdown terminal?
(It’s also possible some setting or extension is interfering with wl-copy’s ability to temporarily get a surface focused, too.)