Alissa,
We do not have one "Out of the Box" that reports total time by Milestone but we do have...
Total Hours Reported by User per Project
Unfortunately, that is the only built in report that would really work for you at this time. We are revamping our Report Module but that will not be available until the end of the year.
The other option you have is to use the Excel Addin. There is a cost but if you use this, you can query any fields in the DB including and show the data by task item, hours, milestone, etc. Then you would use Excel functionality (Formulas and Pivot tables to take the raw data from Clarizen that you queried and create a report that shows you Total hours per user per MILESTONE!
Sincerely,
Boris