I am in the process of reviewing and trying to understand the best way to handle negative score answers. As there's some level of discussion around this topic, you can expect somewhat inconsistent behavior in "low quality" flag handling. If this behavior bothers you, I'd suggest abstaining from flagging negative score content as "low quality."
The general impression that I get from the moderation team (especially through discussions with Grace Note) is that flagging these is not always appropriate. Flags are intended for things where moderators must intervene, and there's a sort of implied urgency in a flag. In fact, one of the canned flag dismissal notices is that flags should not be used on answers which are incorrect or technically inaccurate. The voting system is intended to sort the useful answers from the useless, and there is sometimes some utility in knowing the right and wrong answers to a question.
However, they do represent an issue on the site that (right now) frequently requires moderator intervention. There's a counterargument to the previous paragraph that since there are so few users with delete access, moderators must intervene when something requires deletion, and low score answers require deletion.
For the time being, I'd suggest downvoting these bad/incorrect/unhelpful answers. I am working on a tool that will allow people who can delete (high rep users/moderators) to examine bad, stale answers and aid in the cleanup effort. The side effect of this is that your downvotes will be actioned on far more often, and that manually finding and flagging these answers will be unnecessary.