"No scientific theory has ever explained all the phenomena that fall within its domain."
Of course. Likewise, no piano has ever played all the songs that fall within its domain. There is a gigantically large number of electromagnetic phenomena in the universe, for example; the question is not whether our theories of electromagnetism have explained them all, but whether there are any such phenomena that it cannot in principle explain. The best you can ever say is that you haven't found any; the worst you can usually say is, "we haven't yet figured out how to explain this phenomenon with the current theory".
Okay, but compared to what other kind of "theory" that explains the phenomena better? Astrology? The Olympian gods? Genesis? Taoism? You get the picture.