The -allSites option in GenotypeGVCFs did not emit every position

I was using the -allSites option in GenotypeGVCFs with 100 samples. I found that many positions were missing in the combined gvcf even though these positions have well-supported reference call in every individual gvcf files. I am using GATK 3.6-0. I wonder if there are some parameters I idid not use correctly. Thank you in advance.