Malformation has two forms: Mutation and Deformation.
Deformation is usually due to physical trauma during the early development of the flower (missing or incomplete petal, crumpled flower, etc).
Mutation is when parts of the flowers take on a different form altogether. The most common form is when the petals all look like the lip.
It is a side effect of artificial hybrids.
At a cellular level sometimes things "do not line up" properly because of the multitude of genetic ingredients thrown into the mix. It could lead to some misfires in the meristem growth and cause it to produce the wrong kind of tissue.