I find Yep pretty buggy:
1. Unless I remember not to touch the name of the pdf while I'm tagging it, the tags won't be saved, and there's no warning to tell me this is happening - you just have to notice the doc is still in the "untagged" folder. If you're working quickly to get through a whole bunch at once, it can be pretty frustrating to look up and see some of them have to be done again.
2. Same thing's true when some tags get mysteriously combined into one, like "mac" and "camera" might be combined into a "mac camera" tag, which is worthless, and you have to go back and do it again.
3. There's the "auto-tag" function, which often doesn't work at all. That might be the good news, as when it does, a giant pile of mostly irrelevant tags gets dumped into the file. I suppose it doesn't really hurt anything, since you don't see the metadata later, but it's pretty weird and you wind up having to input the correct tags anyway.
4. Finally, the ability to select non-contiguous files by holding down the command key often doesn't work, and instead results in the prompt to the user: "are you sure you want to combine these PDF's?". Uh, no, actually, I just want to tag them the same way.
By the way, I've tried uninstalling and starting over, with the same results.