From PinataIsland.info, the Viva Piñata wiki
Weeds are plants that have a negative effect to your garden. Some can make Pinatas angry while others can break Pinatas. Weeds, however, are sometimes needed to fulfill a requirement. Nevertheless when they are fully-grown they are added to the Encyclopedia. You can tell if a seed is going to grow into a weed if it is a sinister red and black color.