Zero depths are generally bad, and you should get rid of them. You can either check the option "exclude zero depths" when you are importing track logs, or remove them after import. The easiest way to remove them after import is to use the depth filter - just pull the top slider down a little so that all of the zero depths are greyed out, then press the filter button. These bad depths are likely to be the cause of your phantom hump - you should really always examine your raw data for anomalies, and if possible correct depths in the sonar viewer before using the data as part of a map project.