You could get even 4 alleles.
Like, color of eyes can be one allele, and height can be the second allele.
But when you're doing problems like that which require you to find frequency of occurrence with two traits like that, then you can just solve for the frequency of the each independent allele, and then just multiply the chances.
For example, lets say we are given three traits: color, height, length of hair
C= Brown
c= red
H= short
h= tall
L= long
l = small
You have two individuals with this genotype: CC Hh ll crossed with cc Hh Ll. What are the chances that the off spring will have the following phenotype: Brown, short, and small hair.
Do the punnet square for each trait individually
CC x cc = 1/1 Brown, 0/1 red
Hh x Hh = 3/4 tall, 1/4 short
Ll x ll = 1/2 Long, 1/2 small
Since we're looking for brown, short, and small hair, just take the respective fractions and multiply them together. so we will have 1/1 x 1/4 x 1/2= 1/8
12.5% chance of getting that phenotype.