First of all, the truth is one shouldn’t ask this question. If we have proper Emunah in Hashem we won’t have ANY questions and will realize that as mere mortals we cants understand what Hashem does.
However one major reason many baffling things happen is due to gilgul neshama where neshamos need to come back and get a Tikun as Kapusta mentioned and this is a tikun for things they did in their previous existence.
Kapusta gave a very good answer.