Could the problem be that it asks 'You already have a local version of *logo name* with this sharing ID' when it asks you to replace it - would that mean that if the uploader of the team is different (Casper, fissionmailed, Friedlele7, etc), the sharing ID would be different so it would duplicate the logos of the bats too without asking? Or even within the team, does the academy remember the original sharing ID of the bats as well? I just tried downloading the uploaded Tasmania team as an example, and got almost a dozen Bat Texture Copy logos just from that one team, even though I had said don't replace logos.
I'm guessing at this point it might be better to wait until this is all sorted out before going on a mass downloading session? :-/