Hello. I replaced the upper right control arm with ball joint in my 99 Honda Civic LX. I noticed that the rubber boot on the ball joint went inside when looking towards it (circled in red in picture below).
I took a picture and uploaded it at http://img21.imageshack.us/img21/982/psk7.jpg. Would this cause any damage to the ball joint?

 

It'll correct itself later down the road.

 

How would it correct itself?

 

It'll pop out on it's own, this is a non-issue. The importance of the position of that boot is equally as important as the direction the hairs on your arms are pointed in.