It is not unknown for a watch to cause some discomfort or pain in some cases, normally caused by things like wearing a watch too tight, a watch being too heavy and large on your wrist (which will fatigue certain muscles) or a certain watch shape/size putting pressure on certain points of your wrist and causing pain.
If the pain is occasional, I would look at when exactly it is occurring - is it normally after a certain activity, a certain point in the day or another noticeable trigger? If so look to sorting those out. For example it could be you get the pains after sitting at a computer for a lengthy time, in which case I would look to things like taking off your watch while typing, or looking into more ergonomic keyboard setups. If it normally happens after playing tennis, take the watch off while you play (or wear another lighter watch) and so on...
If it truly is random, then I would probably look to things like trying a different watch for a while (different shape/size/weight) or a different strap, or even just loosening off the strap a notch.
I know with one of my watches if I tighten the strap to where I normally would, it ends up as being too tight, and the weight and restriction of it noticeably fatigues my wrist. Loosen the band a notch and it is fine.
Most importantly though, if you continue having trouble, instead of taking advice from relative strangers (most importantly, not medically trained...) off the internet, speak to your doctor and see what he says on the matter.