One of the plants required for Crop Rotation is Sweet Berries, which can't be planted normally due to the Berry Good mod. Crop Rotation doesn't accept Sweet Berry Pips as a substitute, so the advancement is currently impossible to obtain with that mod installed.

(Also, while not necessary for this issue to be fixed, there are a few more crops with additions from other mods. If you want to make Crop Rotation apply to all of them, the items you need to add by my count are Passion Vine, Aloe Kernels, Foul Berry Pips, Cypress Branch, Strawberry Pips, Vanilla Pods, Mint Sprout, Adzuki Beans, and Mulberry.)