Sometimes it is difficult to install a hinge in exactly the right place. It's hard to hold the hinge in position while you are drilling a pilot hole or putting a screw in. A slight movement in it's position will throw the door out of wack. And once those pilot holes are made, it's a real pain to align the door if they are off. Here's a few tips on how to get that hinge in perfect alignment.
Put a couple dabs of cyanoacrylate glue (crazy glue). Not too much, just enough to hold the hinge in place so you can secure it in place. It will give you the few seconds time you need to align your hinge, and free up both your hands. If you see that the hinge is not set properly you can just lightly tap the hinge off and try again.
Another idea, similar to the first, is to use double sided tape to hold the hinge into position. This will let you drill pilot holes for your screws, again having the use of both hands with litlle risk of moving the hinge while you drill. You'll need to remove the tape before final installation. Even if there is residue from the tape glue, it should not affect finishing as the hinge will be covering up that spot anyway.