are you gluing and screwing. If so, use clamps to bring back into square. When glue dries, remove clamps.
Kreg Jigs are very reliant on mating material that have nice square cuts. Putting a nice fresh cut on the ends of boards is always a good idea. Many boards from home stores or lumberyards may look good on the ends but a few degrees of angle on the ends can definitely throw a box out of square. Also make sure your Miter saw is cutting a true 90 degrees from its fence. Good luck