One thing I've been struggling with almost my entire running life is the second toe on my left foot. It's like the nail catches on my sock when I run, so it gets sore and bruised. It doesn't matter how short I trim it (the nail bed has actually backed up a bit because of this) or if I put on a band-aid or body glide to reduce friction, it still gets really irritated. It doesn't pain me during my runs (thank goodness), but it does get awfully sore afterwards, to the point where it starts to throb and sometimes I can't even have a blanket over my foot when I sleep. I'm concerned that someday I'm going to have to have it removed.
My other toes are fine, it's just that one. It's so strange.