It can happen from time to time that a sync reports an error. There can be various reasons for such errors (file permissions are the most popular one). Unless the error is due to the source or the destination being disconnected, the sync will try to continue until the end.
A common source of errors are hidden system directories like .DocumentRevisions-V100, .Spotlight-V100, .TemporaryItems or .Trashes. These directories are usually located at the root of a device or in your home directory. It is not recommended to backup the entire filesystem (which includes system directories like /Library or /System that usually don’t hold personal data), but rather selected directories inside your home directory. If you still think that you need to backup directories containing one of those protected items, you can exclude them by either excluding hidden files or manually selecting them in the Exclude tab of the sync item’s settings.
It is always recommended to have a look at the error log, which can be opened from the context menu when right-clicking the sync item. The error log provides information about which files caused the error. Particularly for two-way sync items, it is strongly recommended to sync again by carefully going through the confirmation dialog and making sure that no unique file is going to be copied or removed because of the previous error.