I have noticed that the clip or cap inside the headlight housing has come out and is freely moving around. The clip has now scratched parts of the chrome off inside of the housing and I don't believe there is a way to fix this without opening the housing with a heat gun? Would this be replaced under warranty?

Clip came out of here:



Now it's here:



Whole headlight housing (you can see the clip):

 

I see you have a 13 Evo X. So I'd head to the local dealer and let them fix it, should be free =)
Good luck!