Your Linux desktop has two clipboards, and the reason goes back to a 1980s design decision Wayland chose to keep

Linux desktops feature two separate clipboard systems: PRIMARY and CLIPBOARD. These clipboard systems have been a design choice dating back to the 1980s, originating from the X Window System. The PRIMARY clipboard, which holds highlighted text, is automatically updated when you select text in an application that supports it. A middle click will paste the contents of PRIMARY.

The CLIPBOARD clipboard, used for explicit copying and pasting, behaves similarly to the Windows or macOS clipboard, allowing you to paste different text depending on the shortcut used. The PRIMARY clipboard is owned by the application that supplies the data when requested, while the CLIPBOARD clipboard does not transfer data automatically between applications.

The secondary clipboard, SECONDARY, exists but is seldom used. Despite calls for a clipboard daemon to preserve data after an application exits, the design of separate PRIMARY and CLIPBOARD clipboards remains in place.