Most anime/manga focuses on the story and characters, based on the backdrop of the Universe the story is set in. Fantasy worlds usually come with special rules (the "Physics" of the world) that deviate from the reader's reality (e.g. rules of the Death Note, rules of the Holy Grail War in Fate/Zero, law of "Equivalent Exchange" in Fullmetal Alchemist). Should we encourage questions on the implications and contradictions between the rules?
While the rules may appear consistent enough for the reader to accept the fantasy world and focus on the story, it is natural for readers to peer beyond the surface and question the implications of the rules. However, beyond the surface, the rules often contradict each other and do not form a consistent framework, exemplified by the famous plot-holes in time-travel anime/manga. I think it is pointless to enquire deeper into plot-holes, because probably even the writer of the story doesn't have an answer other than "please focus on the story and appreciate it".
In short, I think questions about rules of the Universe that affect plot events should be encouraged, but not questions about why certain rules contradict and form plot-holes.