Translation:I have two questions for the captain.
You'll hear both, so I think voor de kapitein should be accepted, if it isn't already.
I think the fact people also use aan de kapitein is influenced by the fact that the verb vragen can be combined with aan
Ik vraag je iets / Ik vraag iets aan je = I'm asking you something
Ik stel een vraag aan de burgermeester = I pose a question to the mayor/ I'm asking the mayor a question
The translation does not take into account the diminutive 'vraagjes'; the translation as proposed would mean 'ik heb twee vragen aan (or 'voor' which would mean nearly the same here) de kapitein'. A translation like 'I JUST have two questions for the captain' would do justice to the diminutive. By the way, Dutch does NOT use diminutives sparingly, as stated below, not at all! We use them all the time, and even stack them, like 'een klein snoepje' which literally would mean 'a small lillte sweet', but in practice just means a sweety. Similarly 'een klein babytje' for 'a small baby' ('een kleine baby' may seem more appropriate but nobody will ever say that, or just in a negative sense, for instance when you say to an adult 'je doet als een kleine baby'. I guess it's like the difference between 'a small baby' and 'a little baby'). Another gem: 'een heel klein beetje' that means 'just a bit'. Re the red shaded comment below: this is not about mistakes, but about the finer niceties if you really want to understand and enjoy Dutch.
You should use diminutives in Dutch very sparingly. Yes, 'vraagjes 'sounds less threatening, but for an adult it also sounds very silly. So my advice, try not to use '-je' and '-jes' except when you are referring to small sized objects.