That would be a very strange bug. Could you email me the screenshot to email@example.com? Please make sure that you understand: if you delete a file in one sync-ed folder, the file will also be deleted in the corresponding sync folder. The application should have warned that.
Now can you also tell us what type of file is it and which application was used to edit the file? Some application creates a lot of temp files (e.g. Microsoft Office). In this case, FileManager automatically skips the temp file.
Please also let me know which version of FileManager you have, make sure to include the Build Number. Thank you.