Some wild Pixelmon drop items when they are killed. The items will be given to you automatically, so you don't need to pick them up manually. It is never guaranteed that this Pixelmon gives you the certain item and multiple items can be given per Pixelmon (For instance, a Bulbasaur can drop 2 Seeds and 1 Vine, if you kill one, but there also is a chance you get no items). Also, in the chat you will see what the Pixelmon dropped. Here the items they drop (version: 3.1.4) are listed:

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