Penis is made of many different tissues, but, simplifying a bit, we are interested in providing growth to TA and smooth muscle.
TA is connective tissue, pretty much the same as tendons. If you ever trained athletically or with weights, you do know that tendons become larger hand in hand with muscles, but if you have a pain to a tendon, than you have to stop because a bad injury is going to come.
Staying on this analogy, smooth muscle is muscle; when you lift, you can feel (sometimes, not always) an aching, or burning, on the last, fatiguing sets or reps of training: generally, is mostly believed that it’s a good sign, because a little damage to muscles has been provided (if this is true or not it is debatable, but it’s not relevant here); but this burning is never pain in the proper meaning, at least if my dictionary is giving the correct translation :) . So, when doing a very long stretch, you can feel an aching or little burning to your penis - especially when hanging or using an extender; but if you feel pain, then you have to stop, for a reason or another.
A pain when hanging can be caused, in most of cases, by incorrect wrapping or incorrect hanging attachment, so stop and search for the mistake if you are having pain.
Finally, when using an extender you can have bad, but superficially pain, when using a noose-style, especially if you are uncut: that’s not a big trouble, is just skin too sensitive; anyway, noose-style extenders are not generally recommended, so the problem of pain, in this case, is out of question.
If you are having pain using a not noose-style extender/ADS, it would be a good idea posting the pic of the device you are using and explaining exactly what kind of pain you have.