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At https://github.com/hluk/CopyQ/issues/27 the topic Wayland is covered. There are also a few solutions mentioned that you can use temporarily.
I am not familiar with the process at Flathub. But as far as I understand, the developer of CopyQ has already made an appropriate update (https://github.com/flathub/com.github.hluk.copyq/pull/53). Maybe these updates will be shown at flathub.org only with a time delay.
NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a more popular project.