Group and display all applied filters at the top of the Filters section (or above product listings). Allow the user to remove an active filter by clicking on a close (x) button. Also add a 'clear all' link if possible.
Add a 'clear' link above each individual block of filters.
For the engaged user, it is easy for an active filter (chosen facet) to go unnoticed - specially if the list of available filters for a particular category page is very long and multiple filters are active and separated vertically in space such that they are not all visible in the same screen (i.e. some above and some below the fold).
Also, it requires more [cognitive] effort to 'uncheck' multiple boxes in different places on the screen - compared to when they are all neatly grouped together.