Having this issue in Apex 4.1.1 and 4.2 (haven't tried it in versions prior to 4.1.1 yet).
So I got my standard IR, and trying to create a private report with control breaks, aggregations.
Once I save it as a private report, It applies the same on my primary report.
It's no big issue as I can flip back to Primary report and delete the control breaks, aggregations but is some kind of bug? Ideally it shouldn't modify my primary report unless I try to save it as "Default Report Setting".