Consider following proof:
Prove that if $x^2 + y = 13$ and $y ≠ 4$ then $x ≠ 3$.
Proof. Suppose $x^2 + y = 13$ and $y ≠ 4$. Suppose $x = 3$. Substituting this into the equation $x^2 + y = 13$, we get $9 + y = 13$, so $y = 4$. But this contradicts the fact that $y ≠ 4$. Therefore $x ≠ 3.$ Thus, if $x^2 + y = 13$ and $y ≠ 4$ then $x ≠ 3$.
Note the statement "this contradicts the fact that $≠4$".
Definitions from the internet:
Fact: "a thing that is known or proved to be true"
Assumption: "a thing that is accepted as true or as certain to happen, without proof."
Take a look at the first sentence:
Suppose $x^2 + y = 13$ and $y ≠ 4$.
My question is, is it correct that author used word "fact" when referring to $y ≠ 4$? In my opinion, saying "but this contradicts our assumption that $y ≠ 4$" would be more appropriate.
tl;dr It doesn't matter, the meaning is clear and so the usage of the word "fact" is fine.
Long answer: So this a semantic problem. Unlike (most) computer languages natural languages are very heavily context sensitive. And even more: people just love to juggle with words and sometimes they deliberately use words in a non-standard meaning. It makes reading more interesting. The side effect is that sometimes words are misused. And I do agree that in this situation the word "assumption" or "hypothesis" suits the context better than "fact". It's just my preference. But would I point it out as a mistake? Never.
So my point of view is: as long as the meaning is clear and unambiguous then you can use language however you want. For example look at StackExchange. Do we always use words in perfectly correct way? Heck, I'm not a native english speaker, I make mistakes like all the time. But is it really an issue?
Now you've asked in comments "I'd just thought that it might be a problem if you were writing an article or a paper that was targeted at more sophisticated audience". This is a bit different question. Because it asks about possible consequences in a concrete environment. And that is a rather psychological/sociological question. From my experience? It is unlikely that anyone will ever have an issue with that. But is it 100% safe? Well, unfortunately grammar police does exist. But do not overestimate their influence. Also before any paper is published it goes through a review process, so in worst case scenario you just change the word and you're fine. But again: I would be very surprised if that actually happened.
Reminds me of the famous question: what is truth?