I run into this issue from time to time, and I was typing up a support ticket when I realized what happened.
I know I marked all my scheduled tasks from yesterday as DONE in Emacs, but then they were all showing up as overdue inside of Beorg today.
The problem? I had a conflicted copy of my Todo.org file inside my Emacs folder. Dropbox had created a second "conflicted" file, and Beorg was pulling in duplicate tasks from both.
Perhaps we could tell Beorg not to import tasks from duplicate files? But either way, it was easy to fix.
Maybe the better behaviour here for beorg would be to highlight this issue to the user when it sees a conflict file. Then the user can resolve the problem (probably in Emacs using diff to determine if any changes need to be transferred between files).