ok so i just realized that my fingers naturally have really odd alternating patterns....for instance i always lead off with my middle finger, but after that my fingers just go off on there own, for instane sometimes my middle finger will go twice, now the thing is i dont notice this unless i focus on my right hand. ive tried to correct this but its damn hard to do.
eg.
1 = index, 2 = middle
while playing 3 frets in a row i end up with this:
2121221221221221

so my question is will this hurt me in the long run if my fingers alternate in odd patterns?

It may, it may not. Quite frankly, if you can play a riff, I couldn't care less if you use one finger, two fingers, thumb alone, pick, etc. Whatever gets the job done is what ultimately counts. However, if you want to get better at alternating finger-style, you just have to practice it until you get sick or bored with it and then practice it more. Really, that's the only way to really learn anything. I favored my index finger a lot when I started playing. Now, I'm pretty even with alternating with the middle finger. Plus, there are some fast, funky riffs that I play using my thumb, index and middle fingers.

different people lead with different fingers...it's what you do afterwards that counts.

I've just recently included some of my drum training into my fingerstyle and am learning to play patterns like para-diddles and para-para-diddles with my fingers...

It may not be "strict alternation" (for the purists) but it certainly is useful in getting everything to a smooth, quick feel.

paradiddle
1211 2122 1211 2122...

paraparadiddle
121211 212122 121211 212122

try it. it's FUN! :)