This happens because the either the activating app or the app being activated does not implement the Wayland-specific activation protocol (xdg_activation_v1). Both need to correctly implement the protocol.
It’s the same on X11, but apps have had decades to get this right; on Wayland, the protocol is still rather new and a lot of apps don’t yet have support for it. They should. 
So you should report this to the developers of those apps.