after pon filter, vcf variant num increase? gatk4.0.0.0 . I am upset

I creat a pon with one bed(contains nearly 600 genes), and I use this pon to filter vcf created by 17 kinds of bed file(containing different number of genes。 mostly less than 110 genes) , but to my surprise, in the thousands of tumor sampels test, after pon filter, vcf variant num increase in 12 samples(11 number of 1 and 1 number of 2).

I use gatk4.0.0.0
thanks a lot

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