I've just noticed with 2.8b1 that if you're looking at a certain directory on a remote server, and have a subdirectory within that directory highlighted, then do "option->up arrow" to upload, the uploaded file goes into the highlighted directory, not the one you're currently browsing.
I'm not sure if this is expected behaviour or a bug, but I'm pretty sure it is different from how previous versions worked, and I think potentially confusing -- I see a few posts below from people who can't find the files they've uploaded, and I wonder if this is why.
Upload to Highlighted Directory
File an enhancement report at http://trac.cyberduck.ch/ if you want this to be reverted.