It's both a combination of them having too much carbs and too many anti-nutrients (like grains), including gluten, according to Mark's book.
I believe there is some controversy around beans, as I've seen several paleo followers say they do eat beans. And Mark said an occasional use of beans is probably fine. It's when your diet is centered around using beans as your protein source (such as with vegans) that it's not a good thing.
That's my understanding, anyway.