Mine have been pointing out my entire life. My right one points out more than my left. It's really annoying. How do I fix it?

Well, more importantly, what causes it? How can I find out if it starts at my ankle or my hip?

Thats exactly right, in his case ^^ he would need to point the toes slightly in, leg curls holding a dumbell between the feet are great at fixing this because you inherently have to internally rotate the feet to hold onto it.  Reverse hypers with the legs perfectly straight are another good option as are sldl with toes pointed str8 ahead or slightly inward. 

  Most of the time its either weak hamstrings or over powering glutes that cause the feet to externally rotate, either way the answer will still be the same, to strengthen the hamstrings into proportion.  Pnf stretching the external rotators is always a good idea imo, it likely wont stop your issue by itself but it will help your performance and make you feel much better.  The seated crossover stretch, with one leg bent, crossed over the other, and turning back around towards the bent leg, applying pressure with the opposite arm for the pnf cycles works very well.