I'm not aware of problems with CSS3. The only real problem is that it's not ready for use in most regards. Vendor prefixes are pretty ugly, but I personally don't mind using them.
HTML5 is also nor ready for use; so using a JS life-support system is a little contrary to a lot of accepted standards. That's not a complaint about HTML5 per se, though.
I'll let others detail HTML5 concerns. But as a general comment, some folks don't like to see applications mixed with HTML, which is supposed to be a markup language only. I'm not too keen on the structure of 5 (it's quite confusing and not very intuitive, such as sections within sections, H1s in each section, and confusion over where to use <footer> etc.). I can see the point of it all, but fear that it will be too easy to muddle up and get wrong.
I'm not convinced by elements like <nav>. Personally I prefer an approach like that taken by ARIA, where you assign a role to an element.