Part of the problem is that, again, some of these situations lead to literally re-using real-world bigotry when discussing fictional-world things. Consider, for example, the way the "fictional" Varisian culture is portrayed in Golarion. It was, pretty much without exception, every harmful stereotype about the Roma peoples. Up to and including deeply concerning stuff like a strong presumption of criminal activity (that the authors poorly retconned, AIUI).
Or, for a more pointed example: real-world genocide has been justified with the idea that there are different, mixable groups of sapient beings, and that only one set of those is acceptable while others are unworthy of life. It is, quite literally, a core tactic of "ethnic cleansing" programs to portray different ethnic groups as though they were a completely different species. So, if literal, actual genocidal rhetoric does this, it's really REALLY not much of a leap to ask, "So...what's different about this thing in D&D? Both of them designate a target group of sapient, humanoid beings for unchecked violence, often specifically with the goal of occupying the land on which they live and taking away the valuables they possess."
That's pretty uncomfortably close to the way numerous real atrocities were conducted in human history. There's a pretty clear pattern: demonize the natives (sometimes literally equating them with demons!), claim their territory, treat all opposition purely as violent raiding rather than armed responses, trivialize or dismiss all social structures/monuments/environmental management as fake or induced or stolen from someone else, specifically categorize their native religions as horrible and brutal and evil-loving, etc. And wouldn't you know it: the deities of gnolls, orcs, and kobolds are all treated that way (Yeenoghu is a demon lord, Gruumsh is evil, Tiamat is evil); they're almost always native to whatever territory they occupy and driving them out of territory they've occupied for centuries or millennia is portrayed as an unalloyed win for good and justice; they have "barbaric" practices and all their activities tend to be summarized as "raiding" or "recovering from previous raiding," and they never build any temples or cities or roads or monuments, but do occasionally steal such works left behind by long-absent advanced precursor civilizations. And as a result of this list of things, they are acceptable to kill on sight without a second thought.
Note, when I mention these things, I am not saying that someone who enjoys a casual game of D&D where you fight Obvious Bad Guys and save Designated Damsel'd Victims (or take over the ransom yourself, or whatever) is in any way morally wrong. I mean, I've played hundreds of hours of Payday 2, a game where you are literally sitting on piles of hundreds of millions of dollars but continue to slaughter hundreds of private security dudes and public LEOs in order to steal valuable goods or commit election fraud--and I enjoyed those hours of play. I am NOT saying that engaging in a fictional demonstration of a thing with moral question marks on it is inherently bad. That would make me a hypocrite, which I'd rather not be if I can avoid it.
What I am saying is that having these things hard-coded into the game's fundamental rules, particularly when it's all implication without nuance, concerns me. With Payday, I go into it knowing that what I am doing in the virtual space is a fantasy about amoral naughty words doing immoral things for fun and profit. I know where to draw the line. With D&D, that's not as clear. It is easy to say "these species are fictional," but the bright lines aren't present. Unless we do things with eyes fully open, mindful of our choices, it is easy to accidentally internalize thoughts or patterns that may be harmful--to ourselves or to others.
