Unfortunately, it is hard to avoid hurt feelings at any wedding. Inevitably, any event with that much emotion and protocol surrounding it is going to offend someone at some point. Which is not to say that you should shrug that off in dismissal. If you have a very small wedding party which left several people out, or likewise, a very large wedding party, leaving one person out, consider their feelings. Even if you aren't going to invite them to be in the wedding party, try to empathize with them rather than get irritated.
You can include them in a variety of ways. Ask them to man the guest book or gift table. Perhaps, simply ask for their opinion (only this friend has enough culinary know-how to help you pick your cake, etc), and make sure that you let them know it matters to you.