You don't have to worry, it's a rare BOINC bug (but no matter how rare, it does happen time after time to people based on how many people run how many tasks) where in some race conditions there would be a conflict between trying to start a task and a completed task being reported in the same slot (file system folder).
There's a better description of this bug somewhere on forums... Stream definitely posted about it somewhere. And to assure you, "finish file present too long" happens in other BOINC projects too.
Either way, I'm pretty confident you don't have to worry.