For example, if humanity was nuked and alien archeologists found an article of an election in Nevada, with comments joking about aliens in Area 51 voting, how could these historians differentiate that as humor if they know nothing else?
How do we know some aspects of history aren't a misinterpretation of what someone said as a joke?
Especially if these fictional archeologists were to conflate the term "aliens of Area 51" with other terms used, like the archaic version of alien meaning foreigner.
How do we know our understanding of words from ancient languages don't stem from people who couldn't spell or misuse words that had multiple meanings? If you were in the 1800s, alien meant foreigner. In modern times it means an entity from space. How are we so sure of even the definitions of the words we read when language changes century by century?
How do historians get around the unreliability of certain texts in these scenarios where culture shock, the liquid nature of language, and cultural quirks show up? Similarly, how can historians tell if a text is biased at all if the author is long dead and we have no way to know their personality or biases or if they are piecing together evidence that simply does not go together?
Another example is where Futurama kinda plays with these ideas where a museum has Fry's pizza place, with wildly wrong theories about how the the 20th century worked such as the pizza board being a "spanking" device, an account of a moon landing by "whalers", and other misconceptions based on memes of the past and accumulating assumptions of previous historians.
How exactly do we know we aren't just as wildly wrong? Because by logic if the very foundation of our understanding of what we see is faulty, then everything we know collapses too.
There's no magic answer here — historians learn as much as they can about a subject and apply their judgment to it, ideally using multiple approaches to do so. We spend decades learning the relevant information so we can sort out these sorts of things. We rarely use a single text or a single source as the be-all and end-all of our historical understanding, and those scholars that do (like some medievalists) are very careful to try and indicate when they do and don't understand something fully. There are, of course, ambiguities, but even sorting those out can be interesting. Are there occasionally references to things in historical accounts we can't really trace the origin of? Sure, even for well-documented, modern things. They can be interesting to think about, but since we don't really know what they mean, we don't tend to anchor any interpretation in them.
Let me give you an example of the latter from my own research. The Farm Hall transcripts are a well-known 20th century document, the translated transcript of surreptitious recordings made of German physicists at the end of the Second World War, made with the intention of figuring out what they did and did not know about nuclear weapons. Among the pages and pages of content, at one point (before Hiroshima), the physicist Werner Heisenberg says to another scientist:
About a year ago, I heard from Segner from the Foreign Office that the Americans had threatened to drop a uranium bomb on Dresden if we didn’t surrender soon. At the time I was asked whether I thought it possible, and, with complete conviction, I replied: “No.”
After Hiroshima, he brought up the same story, and this time said that he had said that it was possible.
Now this is a weird little thing for Heisenberg to say twice. So far as we know there was no Axis intelligence about the American atomic bomb project, and certainly there had never been a threat to use it against Dresden. So where did they get this idea from? At the moment, we don't know. Was it a rumor? Misinformation? Misunderstanding? Just made up? A joke? Without more information, we can't say.
One can, of course, make some speculative (if educated) guesses. (I have done so here.) And this can be an interesting way to think through what we do and don't know about it. But it's a different thing from being perfectly confident in the truth status of whatever Heisenberg is asserting, or the context of it.
I think what a lot of people misunderstand about the work of doing history is that puzzles like this are what make it interesting. They are not discouraging — much the contrary! We are looking for anomalies — oddities, things that don't make sense — all the time. Because that's where one might have a chance to say something new for once!