This morning, however, when I sat down to a hot cappuccino with my Chinese teacher, she asked me, “有问题吗？” (yǒu wèntí ma?) I was confused for a moment, since I thought she might have been asking it in a challenge way - like "What's your problem??" Then I realised she was simply asking if I had any questions at the start of our lesson.
As I say, most of the time the context makes it clear what your meaning is. But if not, you could always extend the sentence just a little.
For example, instead of "我有问题" (I have a 'question', or I have a 'problem'??) - you could say "我有问题要问你" (I have a question I have to ask you.)
Or you could just leave people wondering about you.