Number One: The big stones are a trouble when felling trees. Logs get stuck in/on the boulders and it is impossible to process the wood without having to eliminate the stone.
Number Two: New fishing system + auto-logout = evil. Me and my mate got kicked several times while fishing or cooking stuff. While I never encountered this bug with cooking or building myself, the fishing really is annoying, especially since it's a rather long process to get back online again. I love the auto-fishing feature, but hate the fact that it doesn't work.
P.S. I am almost sure that some of these errors have already been posted, but since the forums are way too slow to search them in their current state, I won't research into what has already been discovered regarding new bugs. If you wish me to stop, please say so.
Dammit. Kicked again. This is really annoying. Please fix the fishing one soon!