You may see a "duplicates" badge next to some games. This means that some of the same files were also backed up for another game. That could be intentional (e.g., an HD remaster may reuse the original save locations), but it could also be a sign of an issue in the manifest data. You can expand the game's file list to see which exact entries are duplicated.
You can resolve conflicts by disabling certain save files from being backed up. Once a conflict is resolved, the badge will become faded. You can also click on the badge to view just the conflicting games.