Why are there missing calls in a VCF file from exome sequencing?
Missing variant calls due to lack of coverage shouldn't happen in the targeted capture region and I'd think most of these would come from off-target regions where some samples had reads mapped. I'd filter out the VCF to only include on-target loci before proceeding with further analyses.

If you did your variant calling on samples separately and then merged them together, you'll have missing calls at loci called variant in one sample and homozygous reference in the other.

You can get over this by asking the variant caller to emit all sites within the target region, which would lead to a large VCF or do multi-sample calling, which is more computationally intensive. 

One other way is to do variant calling on all samples separately, generating a BED file of all variant regions in the cohort and then asking the variant caller to genotype those loci across all samples before merging them together.