Is doubting God's decree regarding the polytheists entering Hellfire, and saying: "Indeed, God is obliged to preserve the Quran," considered doubt in God's command? And are there miracles in this age?

It is clear that the questioner is afflicted with waswasah (whisperings/obsessive thoughts), and she must repel them and not pay attention to them.

It was reported that what was stated in the first question contains no error, and that what was stated in the second question—that Allah has obligated Himself to preserve the Quran—is true. However, it is not impossible for some disbelievers to desecrate the Mushaf (copy of the Quran) as a way for Allah to entice them [towards their ultimate doom].

As for extraordinary occurrences, their existence is not impossible. They are miracles for prophets and karamat (divine favors) for saints, with which Allah honors them in support of the truth and for the benefit of creation.