It's hard to say what's happening w/o knowing the recipe formulation, whether you're flouring your work surface (and if so, how much) and how you're otherwise handling the dough during rolling. I never chill my cookies after rolling (just beforehand, so I don't have to use too much flour to roll them out), and I usually don't get much, if any, misshaping.
Possible reasons for misshaping are:
1. Dough is too soft when you're rolling it, so it misshapes when you transfer cutouts to the cookie sheet;
2. Dough is overworked (with too much flour added), which develops the gluten in the flour and can cause the dough to shrink and toughen on baking. (However, shrinkage is not so common in cookie dough, unless you really abuse it, because the relatively high qty of sugar in it has a counterbalancing tenderizing effect);
3. The recipe has too little flour in it relative to fat to start, which would cause the shapes to spread more than desired, and often less uniformly especially if there are any hot spots in your oven;
4. The dough was rolled unevenly, so fatter areas spread more than others; and
5. Probably others, but #1 to #4 are the biggies.
I'd say chill the dough more before rolling and handle the dough as little as possible, and see what happens.