Taking a break during your training runs is okay, and can even be an important part of training. For instance, a walking break can increase the distance you can cover on a long run. However, if you pause your watch during a break, you can get into problems. Having done a 20 mile run with 3 hours showing on your watch, you assume you can run 20 miles in 3 hours (9 min/mile). If the watch was paused for 20 minutes for toilet breaks, waiting for people to catch up, changing clothes, etc, you actually did 20 miles in 3 hours 20 minutes (10 min/mile). If you then try to race a marathon at 9 min/mile pace, you will be surprised by how tough it is.
There is a place for taking breaks in a long run; just don't pause the watch! This also means that if you have a GPS with an 'auto-pause' feature, you need to turn that off as well.