Fridge Brilliance: After fighting a group of monsters for the first time, Kiefer says that it's his first time fighting monsters. Caravan Heart comes out, and this makes it seem like a plot hole... but Kiefer didn't fight in Caravan Heart, his monsters did.
Gabo's joining level is a form of Gameplay and Story Integration - he joins at level one and doesn't have a lot of fighting prowess. Of course he doesn't - he is essentially a child and a feral child at that. Similarly, Melvin's starting stats are also rather fitting - he's been sealed away for God knows how long.
Dharma Temple is That One Level for a good reason: Orgodemir knew that it, more than anywhere else, is where anyone who could potentially fight against him would be able to maximize their potential and take it down. Knowing he was actually afraid of the place, of course he would send some of his strongest minions to take it out and keep it locked down as much as possible.
In Disc 2 when Orgodemir seals off most of the world? The levels sealed off are all homes to the great spirits... and Alltrades Abbey for some apparent reason. Acceptable Breaks from Reality? Partly... and to keep people from class-changing to warriors to fight him.
When you have to bench a party member, the excuse behind the Arbitrary Headcount Limit is that the skystone only fits four people. This may seem like an Ass Pull... until you realise that, at one point, only four people ever were in the skystone at once. When the group goes to the cathedral of light later on, Maribel is not with them (Donald instead takes her place) and neither is Mervyn since he is already at the cathedral himself.
While it seems as if only a few NPCs ever seem to have acknowledged things in other "past"s (The Torban player who descended from the Roamers, the old man and the kid from Regenstein who warned Greenthumb Gardens about the grey rain, someone mentioning a frozen ship in the past, the offhand mention of "tourists" in Engow), but one that almost everyone missed: The priest from Labres/Vogograd was actually encountered before the rest of the village, obviously playing Labres/Vogograd's scenario (and by extension Al Adid, which is to the south and can be accessed via the woods) further in the past than that scenario was. So given all you did for the priest, why wouldn't he remember you? He has amnesia. This is actually some meta-fridge brilliance wherein you realise that he could have spoiled several crucial plot details like mistaking Maribel for Aishe.
Why do the portals look so familiar... oh, that's right, they're what Travel Doors look like in a 3D world!
Fridge Logic: Dialac is a desert town that had everyone praying for water. The monsters made an evil rain that turns everyone to stone. 50 years later you are unable to save those people because weather has damaged the stone statues too much... What rain? The town is a desert with a prayer ceremony to summon rain.
You could consider wind damage; however, even more can be found. The strongest man of the village was not turned to stone. He lives in Dialac for another fifty years. Why didn't he move the statues into a building to stop his friend from breaking apart?
Sadly, Clayman didn't think of doing that before he left to find a cure. He searched high and low, far and wide, and took so many years to track it down that by the time he returned, it was too late. In hindsight, moving everyone to safety first would've been a smart move, but he was so shocked and griefstricken at the time he simply didn't think of it. I imagine he beat himself up over that oversight afterwards, though. He had plenty of time then for 'could've, should've, would've'.
This is actually expanded upon in the 3DS version wherein it mentions that the statues were weathered, but not how - one can easily assume they were eroded by sand. This is a desert.
The forces of good and evil fought to a stalemate a long, long time ago. So you'd expect Orgodemir and God to be around the same level of power, no? Wrong. God is the Nintendo HardBonus Boss that far, far, FAR surpasses Orgodemir in every way. Even if you defeat God He brushes off the fight as if it meant nothing to him. How did the conflict end in a stalemate if God should easily have been able to trample over Orgodemir and his forces all by Himself?
Orgodemir spends most of the game expending his power through proxies: the army of automatons, the Grey Rain, et cetera. God's moves in their cosmic chessgame are comparatively minor.
It's also explained later in the game that God actually WON the conflict, but he trusted humanity and the elemental spirits with the responsibility of fixing the world.