Ok, I haven't seen the film, so take what I say with a gram of salt. I have, however, seen a LOT of people TALK about the film and from observing what they've said my take on the "Aliens are just wrong" bit is that it boils down to the following:
"Aliens" while fantastical, and still a topic of serial adventures from the 1930s and on (See also, Flash Gordon, Buck Rogers, etc.), had never been part of the Indy canon. Indy's stuff was rooted more in Republic jungle serials and Doc Samson type stuff. As such, it's decidedly "supernatural" rather than "science fiction." Voodoo and biblical relics all fit within the realm of the supernatural. If you watched the YIJC, you even get vampires thrown in. So, you've got supernatural story after supernatural story.
And then you get space aliens.
It's a bit jarring because now you're asking people to accept an in-universe thing that is different from the established formula. It'd be like the National Treasure franchise doing a third film about, say, biblical relics with mystical powers. You've already established your "feel", and then you change horses mid-stream so to speak.
Now, logically, I think that you can easily argue "WTF? They're both equally fantastical. Why's it matter if one comes from space/another dimension, and another comes from God?" All I can say is that, from what I saw, fans felt that it was just "different." It didn't "fit."
Personally, I suspect another problem was the 1950s setting and the introduction of Commies as badguys. While in real life anyone who studies history will tell you that the Commies of the 1950s were NOT "good guys" by any stretch of the imagination, and that Stalinist Russia was every bit as scary as Nazi Germany, "Commies" as badguys, while historically accurate, just don't have the emotional oomph that Nazis do.
Nazis are synonymous with "evil" in modern culture. Show a guy in a Wermacht (or Gestapo or SS) uniform and give him a faux German accent, and he's AUTOMATICALLY a badguy by default. Commies, on the other hand....well...it's complicated. They were our allies during WWII. Stalinist Russia is distinguishable in many ways from, say, Kruschev's Russia and so on. Personally, I think there's a "kitsch" element to how the public views Communists-as-badguys nowadays. "Oh, that's so 1950s/1980s." Never mind the fact that life at that time was really genuinely scary. I think there's also more ambiguity about "our" side, too -- yes, the Commies were bad, but we were also toppling duly elected governments like Mossadegh's in Iran and Allende's in Chile, and we backed plenty of tinpot dictators across the globe...so are we really the good guys? And, of course, there's the cultural fallout from Vietnam.
By contrast, WWII is a simple black-and-white, we're-the-goodguys-they're-the-badguys cultural moment at its simplest level. So, you throw in Nazis and that's that. They're automatically evil badguys. Anything they want is de facto bad for the world. Commies, though? Not "bad" enough by comparison, I think because of all of the ambiguity associated with the Cold War. Now, as I said, none of this has anything to do with history when you get an understanding. We weren't saints, but the Commies were plenty bad, especially under Stalin. But my point is that the cultural resonance of communism is not as universally experienced as "bad" or "evil" as Nazis are. End result: the commies seem like poor-man's-Nazis, and the film lacks that visceral, automatic "the stakes are high" sense that you had in Raiders and LC. And they weren't practicing human sacrifice like ToD, either.
Anyway, just my observations based on what I've read here and there. More of an outsider's perspective of people's reactions.
