You are correct that brachydactyly is a dominantly inherited disorder and is usually caused by mutations in the BMPR1B gene.
However, not everyone who has the mutation, will have clubbed thumbs (the phenotype). This is due to a phenomenon known as `penetrance` and `expressivity`.
`Penetrance` essentially is an all-or-none phenomenon whereby certain individuals who have a mutation express the phenotype (in this case, clubbed thumbs) and some do not express it at all.
`Expressivity` is when individuals who have the mutation, will express the phenotype to varying extents. For example, only one thumb may be clubbed.
I hope this helped.