To add some context, LayerVault posted a blog post outlining "The Flat Design Era"[1]. While the term has been used before in various context, to me, the post seemed to ignite a lot of discussion in the tech/design community about flat design (and by relation, skeumorphs, etc.,)
LayerVault is a vocal proponent of the "Flat UI" approach and uses it almost as a signature look and feel for their product. In the follow up discussions, the blog post author has said that no post or discussion fully understands what he meant [2].
I can't read the takedown letter or discussion where I am (for some reason github is blocked). But based on what I've seen, the kit is similar to LayerVault's approach to employing Flat UI. That combined with the blogpost, I wouldn't be surprised if LayerVault felt that their look and feel was infringed upon. Obviously, this doesn't mean that they actually were infringed upon in the eye of the law, even if the kit was derived from LayerVault.
As a designer, I can sympathize with LayerVault's issue with the kit (I'm making assumptions), but with such a design, I really wonder how valid their complaint is within the law.
[1]http://layervault.tumblr.com/post/32267022219/flat-interface...
[2]Designer News thread that I have no link to at the moment.