What do you think about the holy prophet's ascent (Mi'raj)? It is only cited in Quran but of course Allah has talked with his messenger during such a mysterious journey, or at least has sent His Angels to bring messages from Him to His prophet! It is almost obvious. It was not like Allah sending an angel to His holy prophet for the angel to take the prophet --peace be upon him-- with himself and show him around, the universe. It was not a discovering journey. If you could accept this then see we are told every single praying is an ascent for the believers: الصلوة معراج المؤمن
Quran as it states is a book for guidance, it is to guide all the humanity up to the Day, all the guidance in one single volume book not so that not every saying of Allah would find a place in the guidance book. Also nowhere it is claimed to be a collection of all messages from Allah to his prophet, but always ,it is stated to be a guidance book, that's all.
The Muqatta'aat phrases in the beginning of some specific Surah are highly encrypted that even the Angel who was the messenger of Allah to His prophet wa not aware of its meaning, but the prophet knew their meanings, so that he should have given the key and the key is not in Quran otherwise the angel should have known about it as well. Allah knows best, though.
@Ahmadi's answer is perhaps the most direct and explicit answer to your question from Quran itself. There are verses in Quran clarifying that the holy prophet --peace be upon him-- was too much submitted to Allah
قُلْ إِنَّ صَلَاتِي وَنُسُكِي وَمَحْيَايَ وَمَمَاتِي لِلَّـهِ رَبِّ
الْعَالَمِينَ / لَا شَرِيكَ لَهُ ۖ وَبِذَٰلِكَ أُمِرْتُ وَأَنَا
Say: "Truly, my prayer and my service of sacrifice, my life and my
death, are (all) for Allah, the Cherisher of the Worlds: No partner
hath He / this am I commanded, and I am the first of those who bow to
His will. [6:162,163]
Explained further in Hadeeth that nothing he said or did unless it was what Allah has expected from him, his will coinciding to the will of Allah in this universe, so that whatever that he says is a saying of Allah, but in His prophet's language.