Add the _JAVA_AWT_WM_NONREPARENTING=1
variable:
Temporary:
flatpak run --env=_JAVA_AWT_WM_NONREPARENTING=1 com.github.reds.LogisimEvolution
Permanently:
flatpak override --env=_JAVA_AWT_WM_NONREPARENTING=1 com.github.reds.LogisimEvolution # Add '--user' if it is installed per user