The omniscient/omnipotent makes even the stuff humans do to each other problematic, but seems much more difficult to overlook earthquakes, genetic disorders, plagues, tsunamis, etc. Hell, even the prevalence of the peanut-allergy should raise some troubling questions.
"Ooooh - dang! Er, sorry about that one Jimmy. I was busy tweaking the binding kinetics of this highly-specific neurotoxin in this one species of parasitoid wasp and forgot to get rid of that epitope on the peanut protein. My bad."
After the Tsunami I was amazed to learn that there were actually (lots of) adults that had seemingly never grappled with some of the more basic implications of the creeds that they'd ostensibly dedicated their lives to abiding by and spreading.
Yeah, right, no person of faith has *ever* contemplated such questions.