Examples I've run into:
1. The current clojure lambda shortcut-syntax is atrocious, and we can do better. Why don't we do better?
2. Clojure could really benefit from a scheme-esque Macro-by-example library. A few exist but they seem largely ignored by the community; despite well-known-benefits to such a system in the normal daily use of macros.
3. A strange hatred of macros. Yes, some people are reasonable and argue that functions should have primacy over macros because of composability (and they're right). But then there are people who will tell you macros are always bad, and if you show up in freenode #clojure to ask for help with them they will actively laugh at you.
I love Clojure and I feel like I know it pretty well, so I'm not trying to say Clojure is considered harmful, etc. But I do think that some of Yegge's criticisms—while poorly delivered and sometimes poorly expressed—have an element of truth to them.
* Full disclosure: I was involved in an effort to write a Clojure book for O'Reilly until I got involved with a new startup and had to terminate my involvement in the effort. I may not be the most unbiased judge of Clojure.