Where others saw invincibility, Rui saw shortcomings.
First, while it was true that Fernan was able to output a huge amount of power from a huge distance away, the way he applied that power was highly inflexible.
The trajectory of the attack was linear. Linear attacks were easier to predict than attacks with a curving trajectory, this was a universal fact. The fact that Rui could effortlessly predict the trajectory of the attack well ahead of time mean that as long as he tweaked his predictive model just a little bit to Fernan's unique situation, it was almost comically easy to predict Fernan to the T
Specifically, Rui looked at his altitude rather than the wings itself. Whenever Fernan prepared an attack, he would stop the rapid flapping of his wings to maintain altitude and stretch them back to launch a powerful wind attack. This caused his altitude to drop just a bit since he wasn't flapping them to maintain his altitude. That was what Rui paid attention to.