It sounds like you have some mismatches between the files. Ideally, when using the auto-upload capabilities in SSI Web, the software will compare files locally with those on the web server, and update what it needs to.
If your study is not live, you might try deleting the study folder where you initially uploaded and then trying the upload again.
If this doesn't fix things, you'll probably need to contact our support team and send in your study (email@example.com). It would be helpful to include a screenshot of the error, and provide us with FTP access to the server so we can take a look.