If the plugins are using CommandSpec (the easy way to create commands) they just need to add .permissions(“example.command”) to their CommandSpec.builder().arguments(…).build() builder chain.
If they implement CommandCallable themselves, they need to implement testPermission themselves.
If the plugin does this correctly, and it’s still not working, either it’s a bug in sponge, or the player really does have permission for the command (maybe they are opped and the permissions implementation gives them the permission?)