Can I ask you if there is something I don't understand?
Is this English sentence natural?
You can ask but that doesn't mean I will be able to explain. In other words, yes, the question works and is acceptable. It is definitely ambiguous and I would never write it (I would hope), but when spoken, the intonation should define what you precisely mean. You should throw in a comma, if you are writing it: "Can I ask you, if there is something I do not understand?" without the comma, the received idea would be that you are asking the person if there is something you don't understand, which may be difficult for the person to answer, depending on what else you happen to have said (you could have just said what you think the idea is, and then asked the person if somehow that idea of yours is wrong, in which case the person might see what it is about your understanding that is incorrect).