Sometimes when clicking a breakpoint in the gutter, a fencepost situation will occur and you'll have to click the line below in order to click your desired line. For instance, you want to click line 113, but you have to click 114 in order for the breakpoint to be set on 113. Scrolling up or down seems to fix the issue.

Thank you for your bug report. This issue has been closed and fixed in git. This change will be available in a future release, but you can download the change at any time from the git repository, found at http://www.bluestatic.org/git/.