Thank you for the additional information.
I guess, this is a Swing/Wayland issue then. I am running yEd 3.25.1 on KDE Plasma 5.24 and X11 without any issues.
To be honest, I do not think that there is much that can be done on the yEd side of things. This is something Oracle, the vendor of the Java runtime environment, and/or the Wayland maintainers have to improve.
That said, there is one thing left you could try (even though I fear the chances for success are not too good): Instead of running yEd with Java 22 (which is older than the bundled Java 23), you could try to run it with Java 24 or even Java 25. Maybe a newer version has less issues with Wayland.