How long have you been doing Squats?
When most people start out, your body isn't used to holding a heavy bar on their traps, so sure, their is some pain for awhile while you get used to it.
If you have been doing Squats for awhile, then perhaps is time to analyse your technique. The most important thing when it comes to weight is technique, especially big exerices like Squats. Ask a personal trainer to watch you Squat and see if you are doing them properly.