I just based my response off of prior experience some pretty safe assumptions:
A) He has job, school, both, or some other outside stress. While I know this is stuff that we all have to train through, certain weeks it definitely takes its toll, during these times I know my head isn't 100% in the game.
B) He is probably not eating/ and or sleeping enough
C) When he stated that he has been on his current program, that the three months he has been on it has been with out a break and has hit the gym with sufficient intensity.
I'm not trying, nor do I have the credentials, to give him a clinical diagnosis of what is causing the fatigue and joint pain. I just simply gave a pretty safe general recommendation of giving the hurting joint a little time off, eating more and sleeping more, which I didn't really feel warranted knowing all of his stats.
just my .02