For 1, the only reason I know for this is if the files were locked and in process. Can you share and filenames or extensions so that we can explore this further ?
For 2, you only get the message at the end for files that could not be sync'd. it does not delay the sync of other files. You should see the list of files that failed to download/upload and the buttons to retry/abort. Each file is tried 3 times before we give up and it is put on this list.