It is a bad habit to pluck the eyebrows which may become loose the skin around the eyes. Then it will cause the dark circles or other symptoms. And the eyeballs will be squeezed. That is why the eyes start watering. You should have a good rest for the eyes.
There are possibly two causes responsible for the problem you described according to some common sense in the field of protecting eyes.
First kind is that when you pluck your eyebrows, accidentally some of your eyebrows drop into your eyelid, without being felt by yourself, but this does make your eyes react by watering.
The other kind perhaps because your eyes are naturally very sensitive to changes of lights and the movement of other things in front of your eyes.
All in all, protecting eyes follows some important manners:
Frequently wahsing your hands before any touch on your eyes.
Having some eye drops, which can relax your eyes after tensive work.