In my book it really depends on two factors: 1) was this a spa massage or a private masseur and 2) how significant was the shortfall. I may ignore an insignificant short fall if the quality of the massage was good. At a Spa you can always speak to the manager about it. As for a private masseur it is hardly ever worth the aggravation to try and discuss with the masseur. A confrontation is hardly ever productive. He will become defensive and that is likely to raise your blood pressure, right when you are suppose to be relaxed from a massage. I usually pay the agreed fee and move on.
The exception is that if the masseur suggests that he would like to see me again when he shows me out, then I would raise the short fall but I will not commit to seeing the masseur again, even if they offer a discount for a future visit. "Look, you seem like a nice guy and the massage was good, but it was supposed to be 60 minutes and we were done in 45 minutes. You may want to keep a closer eye on the agreed length of time..."