punnet squares are an oversimplfied explanation of the probability of inheiratance of any one allele. in the case of the 4x4 matrix the typical application is dominant alleles vs recessive, relative to each other.

first problem is that 2 alleles is a simplistic example for the purpose of disseminating the concept.

there are, more often than not; more than 2, due to variation. there are normally only 2 chromosomal loci to correspond to an allele, but more than 2 alleles exist.

2nd issue is expressivity and penetrance of allele.

  an allele considered to be dominant over a recessive allele may be silenced due to factors beyond sequence at locus.  a second gene[s] may influence expression of this first gene such that the dominance/ recessivity is side stepped by a silencing relation ship of a second gene, upon the first [dominant] gene, leaving the recessive allele to express product in lieu of the normally dominant allele.