Beans (like grains) have a lot of phytic acid in them. Phytic acid prevents the absorption of minerals. The amount of phytic acid can be reduced if the beans are soaked in water that contains lactobacilli for a day or so, but almost no one does that.
Not just phytic acid, but lectins and all sorts of nasties. Red kidney beans are poisonous unless you soak them properly before cooking.
There are aspects to beans that are hard to digest, and may inhibit the intake of some nutrients... that said, I'm not hardline on paleo, I do try to keep my net carbs under 100g/day, and consider my diet paleo-ish. I usually have a couple some eggs/sausage, lunch is usually a savory crepe (low carb wrap essentially), and 8-16oz of greens at dinner (huge salad, with a nominal amount of dressing).