At work, we use a bug tracker called Pivotal Tracker (www.pivotaltracker.com) that allows engineers to file features and bugs. If a feature or bug fix is delivered, it is QA's job to accept or reject it accordingly.
If an engineer implements a new feature that has a bug in it, should QA accept that feature and file the bug separately, or should QA reject that feature and report the bug in a comment?
Potential advantage of rejecting the feature: Better chances of engineers noticing and fixing the bug before releasing the code
Potential advantage of filing a separate bug: It allows engineers to better assess how many bugs there have been (if that is really useful)