I enabled around 4 pwm channels in pic controller and found that 3 are working but 1 was not working. I replaced the controller with another spare controller and found all 4 channels working. So my general question is it possible that only 1 pin will malfunction? How to identify such situations?
Sure; something (electrostatic damage, a short circuit, a load which draw more current than the pin is rated for, etc.) may have blown the pin's output driver. This happens from time to time.
Exactly the way you did: try a spare part and see if that corrects the problem. Also, examine your circuit to see if there's anything in it that could exceed the pin's maximum load current specification.
I've mentioned previously on these forums, that I once (a long time ago) did just the same, and actually have my fingerprint melted in the top of the PIC - which is still fully functional