Answer: Guessing the outcome of mice's fur is not foolproof. Punnet squares are just based off of probability and cannot actually predict the outcome of a mouse's litter. Just because dominant alleles are present doesn't mean that the recessive alleles won't appear as much as the dominant ones.
The results of the mice are different from the expected ratio because alleles assort independently in gametes at the time of gamete formation. Although, we can check the probability of the alleles the offsprings from a cross will carry, but we cannot exactly tell that which gamete will acquire which allele. Hence, the ration through a punnet square is just an assumption. The actual values might defer as alleles assort independently.
