I am doing some imputation job in Beagle and after phasing and imputation I am getting some individuals having duplicated lines for some SNPs but with SNPs phased differently e.g. an individual with 0/1 for a SNP before phasing ends up with two lines in the vcf file, one with 1|0 and the other 0|1. See a simplified example below for one individual and one SNP.
VCF file before phasing
#CHROM POS snpID 344 1: 9 103 Bovine9 0/1
VCF file after phasing
#CHROM POS snpID 344 1: 9 103 Bovine9 1|0 2: 9 103 Bovine9 0|1
Any help on what could be happening here, is this usual?