Early on when you first encounter the legion by storyline I was wearing NCR armor, and I thought they were hostile naturally, I killed them and it told me I failed 2 quests, and that the legion hates me and vilified me.
Is this going to be an issue later on?
Well. Not like most people would know but for those that do.
It's not quite an issue. You'll lost some minor side quest from the beginning, but it's no big deal.
Plus, later on, iyou'll get the possibility to reset your reputation with them.