That is actually not a problem. She still stuns that unit and she will be immune to everything when doing it. In some situations sure, it should be better if she used it on the low hp unit she is fighting but in other situations stunning the other nearby unit can be much more beneficial.
However what happens quite often is that Fiora starts channeling her spell and the target she was fighting (or rather which the spell chosen already at the start of casting) dies and she ults into void stunning nobody despite there are other targets close she could stun.
BTW just won with Fiora carry team. Got t3 Fiora before golems, on top of that I started with BF and got tear, bow and rod so I put it all on her, rageblade + SoS, she solocarried all matches in early/mid game. At raptors I had spare cloak so I put it on her and I was able to take another BF from carousel which was BT. And if she somehow got low, lulu ulted her and she kept going. In the end, I lost 3 times in row against 3shapechanger/6sorcerers team, but after last carousel I was finally able to roll third Draven and the imperial buff were applied on him. With some luck of mana draining his t2 aurelion by demon spatula lulu, I was able to win against his t3 Shyvana with 3 items.
so yeah t3 Fiora with
or
can do wonders. Well at least with Shen and Lulu in same team :)