Differences between WES and WGS is limiting the HC to an interval

Limiting your calls with HC to an interval, e.g.

-L a_bed_file_containing_intervals_of_the_exome.bed

exome captures are not 100% efficient. so i would guess that you are getting calls in regions of non-specifc hybridization as well as regions that are slightly outside the exome (due to probe design and/or sequencing chemistry/strategy).