There are things we now understand better (or not!)
Not everything is a single gene trait; multiple genes can work together to influence an observed phenotype, such as yield or plant shape.
Turning that statement around, genes at different genomic locations can affect the same characteristic, such as fruit color or epidermal hairiness.
Genes for different traits may not be inherited independently (i.e. they may be near to each other on a chromosome and tend to be inherited together). That will skew observed phenotypes from Mendelian ratios.
Those are some of the things that can complicate expectations, but keep genetics interesting
