Polydactyly is an inherited condition in which a person has extra fingers or toes. It is caused by a dominant allele of a gene. This means it can be passed on by just one parent if they have the disorder.
Interestingly, not all ancient giants were found with six fingers or six toes, just a fair portion of them which denotes a sense of small community to breed within and consanguinity (inbreeding). It is not that their sub-genus of man naturally had six fingers, but that conditions for breeding were such that a good deal of their population was cursed/blessed with extra digits.
If you had a few dozen people who could not breed outside of their subgenus and the dating pool was the small community of options, traits would be passed by both parents.
This is like redheads. It takes two parents who carry the redheaded gene to produce a redheaded kid. In the case of polydactyly, with both parents carrying the gene, this will become much more prevalent in the population.