One thing particularly annoying for me is HTTP Proxy: it seems that as of Public Beta 2 setting it will cause the device flood the server with many requests. I'm using GlimmerBlocker and on the server side it'd get 1k+ threads almost instantly after I turned on the proxy setting on the iOS side.
Other annoying bug is WebKit View would lose width setting randomly in 3rd party apps (e.g., Reeder).