If we see one in an unimportant folder, we move it temporarily to your Inbox at the end of the day. We assume you flagged it because it needed some followup processing. And where better to do that processing than your Inbox.
If you signed up for SaneBox before October 9, 2015, this feature is turned ON by default.
You can toggle this feature on/off by visiting your "Advanced Filtering" section of your Dashboard.