Fantastic Racism: In the universe in general, in many places. Species vs. species, meat vs. metal, augments vs. baselines, oxygen-breathers vs. methane-breathers, elder races vs. younger races, oh, and let us by no means forget the good old intraspecies kind. While not all species evolve with xenophobic jerkery coded right into the genome, enough do that this particular meme just keeps coming back.
The Imperials, by and large, eschew old-fashioned racism in favor of traditional Cultural Posturing and, in particular, sneering at the unContracted. Well, except for the Purity Crusade (who want to wipe out all non-eldrae, or at least non-Imperial, sophont life for being, essentially, a bunch of defective entropy-worshipping slave-cultist creepazoids and therefore not to be allowed to exist, especially if it might one day threaten its betters), but they’re a tiny group of, essentially, the whackos’ whackos.
Uncanny Valley: Largely averted where other species are concerned, simply because they’re far enough apart in appearance from each other that it never comes into play. (Now, eldrae and humans, both being humanoids, are probably close-and-yet-far-away enough to fall right into this where each other are concerned – proportions off, and yet too perfect, too serene, move too smoothly, body language is all wrong – yet another reason why I don’t plan on touching that particular First Contact.)
A recognized phenomenon in robotics design where androids and gynoids are concerned; mostly averted in practice because it is a recognized phenomenon, and so cybershells of this kind tend to be either very, very good indeed, or deliberately robotic enough not to trigger it. And if you really want something that looks that human species-like, you can always go bioshell. Of course, much the same thing applies to bioshells with certain types of extreme augmentation, which their designers have to take into account.
This whole thing, of course, is all inconvenient enough that it’s an instinct the bioengineers are working hard on ripping out through their xenophobia elimination program…