Some games (and not only games) contain references to popular books, films etc without identifying what they're referring to, probably assuming that it's popular enough for the player to know.
Would it be off topic to ask what a particular reference is about? For example:
In ThisGame, the main character Bob says "It's a bird! Oh no, it's a plane" and Alice laughs and says "Are you sure it's not a humanoid alien?" I think it's probably a reference to something, but I don't know what. What does it refer to?
(The above refers to Superman.)
Addition after some comments:
Would it make a difference if no character reacted to the reference, including the one who said it?
In the example above, if Bob had said "It's a bird! Oh, it's a plane. How strange, for a moment I thought it was a flying man" it would still be a reference to Superman, but nobody in-universe would have recognised it. Now it's not a character making a joke, but the creators.