In the garden, the harvest tool seems like you have to align it differently on the patch than the other tools (lower, and more right) to get it to work.
If I clicked in the bottom right of the patch it seemed to work pretty consistently, but that was just from one harvest batch. Before that I was just clicking around. Maybe it really is random, and I'm just making fake consistencies. :)
I wasn't able to reproduce this, though it's possible that it got fixed between the time you posted it and today. I'll see what I can figure out with regards to this issue, and I'll be doing more testing on various platforms in the coming weeks, so hopefully something will come up between then and now. Please update this thread if the issue continues.