For me, it isn't even just males in yuri. I feel exactly this way about love rivals in general, which is why love triangles are so hit-or-miss in my experience. Far too often, they only serve to force development of the main couple and don't stand on their own as characters.
It's particularly bad if it's an Ex that plays the third wheel. Usually, the reader is told all the various flaws the ex has - so you already know they aren't "right". Then the protagonist for some contrived reasons still does something with them (or at least their love interest thinks they do). So either you've got a misunderstanding that's too stupid to believe or you have a protagonist that's too stupid to believe.
And while real life people of course regularly do stupid things it doesn't make for good fiction, usually (some self-sabotaging characters can be appealing, but it needs to be done well ^^; ).
In this specific instance, I'm also bothered by the character's nature as a Chekhov's gun; it was obvious he was going to come up again, and his lack of any real importance up 'til now just makes me doubt that he'll be incorporated organically into the plot. Of course, I'm hoping to be proven wrong.
Very true. However, I think you're also pointing out why it's so difficult to do this right in fiction: real life, everybody runs in a few dozen people each day. If somebody were to observe you, they wouldn't automatically know which one is important.
In fiction though, you only get the high lights. All characters need to serve some function, otherwise they shouldn't be in the story. But then, in romances, there aren't that many options of what they can be there for ...
Balancing this is a tough task to give any author, I think.