It can mean 'of your question' (soru-n-un), 'of a problem' (sorun-un), of 'a question' (soru-nun). You can understand it from context, though in some cases the distinction can be vague (as in English, note that sorun sometimes is also translated as question). In a var/yok-sentence the tricky thing is this: you have a problem - sorunun var, you have a question/there is a problem - sorun var. In the second case, it would rather be asked as a question in case of which the difference would be very arbitrary (sorun var mı - do you have a question vs. is there a problem?). To rule out confusion you could say sorunun var mı if you want to inquire whether someone has a problem (rather than a question).
You may be too young. American astronauts were famous for remaining cool under pressure. When the Apollo 13 mission to the moon ran into technical difficulty, one of the astronauts on board addressed mission control (located in Houston, Texas) with the phrase, "Houston, we've had a problem," in a voice that betrayed no emotion. In popular imagination, the phrase quickly became simplified as "Houston, we have a problem" and came to symbolize understatement in a crisis (and was used in the film Apollo 13). It is still sometimes used to get a laugh (by English speakers) when something goes wrong. https://en.wiktionary.org/wiki/Houston,_we_have_a_problem