@Pulse thanks for your attention. Unfortunately, formatting the USB drive is not a solution to the problem. It's simply a crude recovery method (to a problem which shouldn't be happening in the first place) not to mention a poor user experience.
If the unsynced files are erroneously taking up space on the drive, and thus preventing other wanted files from being synced, then the Sync Manager is clearly inefficient and flawed.
If instead you say that emptying the trash bin is the solution, then please answer this (I'm a Windows user.): On Mac OS, when you unsync songs in the Sync Manager, do they end up in the trash bin? If no, then empying the trash is not a solution. (On Windows that is certainly not the case.) If so, it would be a less serious problem, but still only a workaround at best, and not a solution to the serious inefficiency.
The Sync Manager should handle everything. This shouldn't be an issue in the first place. It should just work.