I am also experiencing this, and it's quite frustrating! This seems to be a cross-platform issue, as I'm seeing it on Mac OS X.
In my case, the package that was triggering this bug was Modific, which I had set to use a standard icon ("bookmark") in the margin by using the "region_icon" key in its settings. Oddly, when I remove that override and allow it to use its own custom "modific" icons, the problem goes away for me. So perhaps it's something to do with the "bookmark" icon? It looks like sublimeclang isn't using any margin icon at all, though, which makes that explanation unlikely.