I'm still not sure what you are saying is going wrong - so, is it that whenever you get one of the quests it reveals all three of them? I can't really test your game out to see what is happening since I don't have most of your character graphics, but from my cursory examination of the events I could find (kind of hard since they're all blank) - the Ariem and Deku events looked fine, from what I could see. The Ilian event was OK except that you use square brackets instead of round brackets (should be $game_party.quests[3].reveal_objective (0), not $game_party.quests[3].reveal_objective[0]). But that would cause a syntax error, not the error you are seeing.
My guess, if you are seeing them all show up (and I assume the other two don't show any of the objectives, just that they are there), is that you are doing a conditional branch check on them in some parallel process event maybe? It will show up the moment you do anything to it, so any conditional branches or whatever would make it show up. I can't really find where it's happening though without being able to test the game, but maybe you remember?
If you can't remember, then there is a way to just avoid the issue and not have to find where you are accessing the others; in the quest guild, put a script call like this:
q = $game_party.quests
q[1].concealed = true
q[2].concealed = true
q[3].concealed = true
(make sure wherever you do this event that it can't run at any time after you've accepted any of the quests)
Then, when you accept quest x, put in this code:
$game_party.quests[x].concealed = false
This method is kind of a lot of work, which is why I made it so that simply accessing the quests would reveal them in general, but if you can't find out where you are accessing the other quests it might be worth doing just to avoid the frustration.