So is it broken again or is it only for certain posts?
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Despite the fact that the Citizen Patrol badge got awarded multiple times in the last couple of hours, there's a good chance that this is related to the fact that Stack Overflow is currently moving its databases. (source)
However, if you only flagged two comments so far, it would also explain why you didn't get a badge.
The description for the badge simply says:
In this context, post means question or answer, but not comment. (source)