Whats happening is that pet commands are no longer queueing.
Before, if Garuda was casting Wind Blade and you hit Contagion, the move would "queue up" and Garuda would cast it on the next available GCD, without further input. Now the input just comes back as a command error unless you press it in between pet GCDs.
So to use Whispering Darn you have to hit it during that split second when Eos isn't doing anything in between Embraces. Same for Contagion, you have to hit it in the gap between Wind Blades or it won't register.