Haha! I missed a Ponyta in the beginning of the game, and it really bothered me. I ran out of balls, and purchased more balls there and then, but my Ponyta was gone. It would have been a new pokemon for me at the time, and I kept coming back to that place to see if it spawns again, to no avail
I later kept a supply of great/ultra balls, just in case, so that next time I see a rare pokemon, I have enough ammunition to fire at it, but actually rare pokemon are so bloody rare that I no longer bother... I just use up all the balls if I feel like it.