In the sweet pea crossing experiment by bateson and punnet, the f2 generation had many more offspring with the phenotypes of purple flowers p, long pollen l and red flowers p, round pollen l than expected from independent assortment. (the parental cross was between ppll x ppll plants.) the f2 generation can be explained because

The F2 generation can be explained because the alleles for flower colour and pollen shape are linked.

Explanation:

When two alleles are linked on the same chromosome, there is a high tendency for the alleles to be inherited together. Consequently, the frequency of the alleles recombining in subsequent generations is low.

This is what Bateson and Punnet observed. There exist a linkage between P and L alleles and also p and l alleles, thereby increasing their frequencies  of occurring together and decreasing the frequency of their recombination.

Thus, the F2 generation observed by Bateson and Punnet is due to linkage of alleles.