What the actual hell. The minimap = total crap.

The forums suck. Literally, it just took me half an hour to actually register to POST on your damn forums... I already have an account logged in, yet you make me register again for the forum and then put a seriously mundane character selection to post? 0.o This game is so beautifully polished yet let down by some seriously frustrating things.

One major thing being the minimap.

Who designed it... this is the worst navigation/mapping system I have ever used. Ever. Period. Monkeys could design a better navigation system.

I literally have a quest marker telling me to go to one location when I ZOOM in on the map it tells me the marker is in a completely different location...

It tells me NPCs are in places they simply aren't and I've had to use rather stategic and ingenuitive ways of finding myself round. E.g. Using one of the seemingly endless amount of screenshots/images other players have posted helping people get round because we all unanimously agree that....

THE MINIMAP SUCKS!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Pretty sure it's just bugged. I've never had it show an objective as in the wrong place. The only issue you may experience is that it doesn't tell you how high the object is within the map space, so if you have two elevations both in use at the given x,y coordinates, it may be in either set, thousands of feet apart (see Sea of Clouds, in Heavensward). Also note that quests are organized in your journal based on where the quest was picked up, not necessarily based on its destination.

Have you tried verifying the installation?

If you're really having that much trouble:

Press M or Square to pull up the full map.

Download the FFxiv Librea Eorzea app, published by Square Enix. It will tell you the exact Coordinates of Npcs, for each specific quest.