The reason beans are not considered Paleo comes down to omega-6 fats and antinutrients like phytic acid (a.k.a. phytates) and lectins.
Paleo and PUFAs
Omega-6 fats are a type of polyunsaturated fat (PUFA) with inflammatory properties. One of the biggest problems with the current Standard American Diet (SAD) is that it is much too high in omega-6 fats and low in omega-3 fats (another type of PUFA with anti-inflammatory properties). Ideally, we should be consuming at least as much omega-3 as omega-6 fats, if not more, but loading up on the beans makes this very difficult.
Being seeds, beans and legumes also come armed with anti-nutrients, including phytates and lectins, to protect themselves against predators like us. Lectins punch through the lining of the stomach, letting toxins and undigested foods into the blood stream and setting off an immune reaction that includes inflammation.
Phytates bind to minerals to prevent them from being absorbed by the body, so even though beans come loaded with nutrients, our bodies are unable to access those nutrients. Phytates inhibit our mineral receptors, leading to nutrient deficiencies.
Getting The Most Out Of Your Beans
By soaking and sprouting your beans before eating them, you can get rid of some of the antinutrients, but not all of them. Mark Sisson decided beans and legumes can be included as an occasional cheat, but they should not make up the bulk of your diet.