Alright then. Here are a few, putting aside the one about Belthasar's omniscience:
▬ Who or what, exactly, is the "Entity" that supposedly held sway over and manipulated just about all the events that took place in the Chrono world?
▬ How was Porre able to overthrow Guardia, in the span of just twenty years?
▬ Kid's oh so special and magical pendant, turns out to be not so special, much less magical. It's supposed to keep Kid from being a victim of lethal injuries or any sort of life-threatening danger by taking her back in time to a safer point in time. Yet it doesn't, ever; not even as much as a little nudge or a spark or anything. She falls off a cliff, get's poisoned, stabbed and apparently brain-washed, and then falls comatose after trying to handle the Frozen Flame.
So really, what the hell was the point of saying it had such powers?
▬ Why on earth did FATE --Lynx, Dark Serge, or however else you wish to call it-- try to drown and thus kill Serge, the arbiter and its only key to reach the Frozen Flame, in 1010 A.D.? It makes absolutely NO sense, and NOTHING is said anywhere which would even attempt to explain such a moronic and contradicting move by FATE.
▬ How in the blue hell did the Earth deity pull back in time a civilization of Reptites (see, Dinopolis) from a dimension that didn’t even exist, as a countermeasure against Chronopolis? Go Earth and its half-assed omnipotence.
I know a couple more, I'm sure, but I have to search my memory a bit.