You're assuming Skarner's stun went off before it actually did.
His E is a slow, not a stun, so the first attack is fine. She queues up Lunge, and probably issues an attack move click right after, before Skarner has even completed his auto for the second attack. It's important that she Qued this up, despite actually attacking second; this is because Skarner stun has a cast delay.
So while Skarner did Auto her for the stun, she was able to attack before the stun had stopped her. This isn't because of Fiora, it's because of Skarner stun.
A similar example, would be if Skarner E+AA Katarina, Katarina would still have a brief period of time before the stun applied, to cast Shunpo. Even though she would be able to move in this time and teleport away, once landing at her location, she would become stunned. At first it seems mindboggling, how she could possibly Shunpo while stunned, but that is because she was not stunned. Yet. Think of the 1s stun, as simply having a .1s delay once triggered, to actually apply.
So even though Pants hit his Auto just slightly before her, Pants Auto did not apply stun before her second Auto was issued and completed in this period of delay time before the stun applied.
In any case, it's 100% an interaction with cast time delay of his actual stun, and not Fiora. You can recreate this issue many ways with other Champions, like how I did with Katarina, his stun just simply isn't instant from the moment he autos and takes some extra time to work.