Avoiding over-mixing when using a stand mixer

It could be a lot of things. Cookies in a stand mixer can suffer from gluten production and there would be no really good way to reverse this effect. However, if you are not mixing the cookies for more than a couple minutes, this is not likely the issue. Other things can effect the texture of cookies that might be a byproduct and not a direct result of the stand mixer.

One example might be that the solid fat that is used in the recipe was over mixed or out too long. Soft fat will make a denser crisper cookie. Refrigerating the cookies for a while would help fix this issue.

Another cause could be a minor substitution. See the blog link below for how different substitutions affect a cookie recipe.

http://www.handletheheat.com/the-ultimate-guide-to-chocolate-chip-cookies/

Along with the above make sure to check things like the expiration date on your baking powder. They lose potency pretty quickly after expiration. This could also cause dense cookies.

One technique you can use to minimize the amount of mixing needed is to put all the dry ingredients in the mixer and let them break up and blend before and liquids are added.

Separately in a bowl, scramble or stir you eggs and mix any other liquids together. While the mixer is running, pour the liquid ingredients in and use a spatula to keep the dough from creeping up the sides of the bowl.

If you get dry crumbs at the bottom of the mixer and need to mix more, then it really means you need to tune your mixer so that the mixing attachment is closer to the bottom of the bowl. A properly tuned mixer should push a US dime (ten cent piece) around then bowl a little bit at a time. This assures that the ingredients at the bottom of the bowl are being mixed and picked up by the wet dough.

Because you say the recipes work fine when you hand mix them, I'll assume that your issue isn't aging ingredients or substitutions.

Honestly, I'd say that running it on the slowest speed is probably part of the problem. A higher speed for a shorter period of time is probably going to incorporate ingredients better because they get thrown about more.

With my Kitchen Aid, I generally start cookies by creaming the butter and sugar together on medium-medium high (6-8) for 2 minutes. Then adding the eggs and liquid flavorings (vanilla, almond extract, etc) and beating until combined.

In a separate bowl, I will have combined all of the "dry" ingredients (flour, leaveners, salt) by whisking them together to aerate the flour and mix them (I rarely sift flour).

When the wet ingredients are ready, I dump in the dry ingredients and start the mixer on "stir" to keep the flour from flying out of the mixer and, when mostly incorporated (10-15 seconds), I'll bump it up to medium low (4) to fully combine (20 seconds). If there are other ingredients like chips or nuts, those will get a quick stir in at the very end (5 seconds or less) with a last turn with a spatula to make sure everything is incorporated.

Using this method, I've never had an issue with tough cookies.

Cakes are more difficult to explain because there are vastly different methods but I'd encourage you to try a higher speed, shorter duration mix in of your dry ingredients.

for a light and fluffy cake, i mix all ingredients in my stand mixer slowly and thoroughly, pushing down the sides with a rubber spatula until everything is wet. then i mix on high for a few minutes, imparting air to the batter for a taller, lighter cake. works for me.