HI, im learning to play guitar, and struggling to fit my 1,2 and 3rd fingers between the frets on an open A chord. I can fit my 2,3 and pinky in alot easier and it feels fine. Will this cause me problems in the long run ? When i use my 1,2 and 3rd fingers i get a horrible vibration noise off the fret.
That may well help in the long run when it comes to barre chords. You use your 1st finger for the barre and move an A shape chord up the neck to form other chords there; very useful for those too lazy to learn "proper" chords.

*edit* As a general rule, if it sounds good it is good. There are, of course, exceptions, but it works 90% of the time.
use your 2nd, 3rd and 4th. It will help you if you jump to a barre or power chord next as well.

EDIT: I'd practice what my comrade above said as well.