Presenting a universe in which LGBTQIAP+ people do not exist is heteronormative and queerphobic. Every time. It is a problem.
It is a flaw.
It would be if you were presenting a universe like that, except you’re not actually presenting the whole universe when you write a story, you’re presenting just a fragment of the setting.
Any story can include any person or thing, but to actually be a complete story that you can write down it has to have a beginning, middle, and end, in a finite period of time. So it can only have a finite number of people and things. Definitionally, it must exclude an infinite number of things just to exist as a complete story.
If I have a story about a tongan cis bisexual and her black genderfluid friend that’s mostly into guys, and they play chess all afternoon and talk about interesting things then they go to make a blueberry pie but the materials aren’t in the kitchen so they have to try cooking with alternate materials and it’s tense because they don’t know if it’ll work out or not. Is that a transphobic story? No, there just aren’t any trans people in the story. Is it a story that’s harmful to autistic people (which doesn’t really have a specific word as far as I know)? No, there are just no autistic people in the story. Is it a story that denies the existence of the schizophrenic, the dysthymic, the bulemic, the anorexic? No on all counts. It’s just a story that is about two people I know and that is not about any of the other six people that I know. They’re all real people and they all deserve to have stories told about them, but not every story is actually about all of them. That alone doesn’t make any of the stories flawed.