In most modpack configurations, Lilypads of Fertility do not work with Botany Pots

Specifically, with the popular addon (which adds higher-tier pots like Diamond, Netherite, and Soul), the mechanics can get confusing. You might have heard rumors that growth accelerators don't work with pots. Others swear that the Lilypad is a magical exception.

Even if the pot contains a wheat crop, the physical block in the world is still a pot. The Lilypad sees a pot, not a crop. Therefore, it skips it.