I've always had an issue with the case of the Quran having "miracles" in it.
Think about it this way. If the Quran had an irrefutable miracle in which it is 100% certainly true, then everyone would become a Muslim. If this happens then there really is no test. Allah stated that life is a test. DO you really think Allah is going to give us the answers to the test, or do you think Allah wants us to strive hard and study hard in order to pass this test?
Given this, Quranic statements must be sufficiently clear to guide someone with an open heart to Islam but at the same time, they must be sufficiently vague so that it does not guide someone with a closed heart who refuses to extensively study the Quran and find the answers.