hmmm….my initial thinking is that this may problem may relating to the hip depth, which is the distance between the natural waistline and the hipline. The normal range for the hip depth is 7″-9″ but with pattern companies they pick a standard and then stick to it in the drafting of their patterns. So, for example, they may say that the standard hip depth for their patterns is 9″. If your hip depth is a little shorter than this, because maybe you have a shorter torso, than their hip depth is possible too long for you and, especially, if the pants/shorts are fitted between the waist and hip, you’ll have excess fabric here which may cause the pockets to stick out. If this is true, then your crotch depth may also be a little long as well. If on the actual pattern, they mark where the hip line is, you can fold the pattern up a little bit to move the hipline up. If you do this, you’ll also have to blend the hip curve to make it a smooth line to the waistline since folding it will probably make the side seam line look a little disjointed. Hope this helps!