Darwin acknowledged that there were important holes in his theory of natural selection. What is the "hole" described in the film?

The hole is  lack of  knowledge of the concept   of natural selection, especially  its physical properties and how  it operates.That is  what made  those organisms with fitted traits  to resit the selective pressures and therefore survive than others with less resistance .

Basically,he lacked the knowledge of the concept of variation as the driving  mechanisms  of  natural selection he theorised. Darwin  did not  understand  how variation among different species of organisms physically emerged to made  these organisms  resistant to the selective pressure,  and therefore   emerge as the  survival of the fittest in the population.

Explanation:

this is math not biology xd