From the Super Mario Wiki
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A nubbin is an inflammation-like protrusion that is found throughout various locations inside Bowser's body in Mario & Luigi: Bowser's Inside Story and its 3DS remake, Mario & Luigi: Bowser's Inside Story + Bowser Jr.'s Journey. In order for it to activate, Mario must hammer this object in order to make something beneficial happen, like opening blocked areas, firing cannons, making platforms appear, etc. They seem to be mostly red to match the tone of the flesh inside of Bowser, but sometimes a different color scheme (i.e. purple, in the Nerve Cluster) will appear, which can cause a different effect from the regular nubbins (like powering up Bowser, giving him new abilities like the Sliding Haymaker). There is also a nubbin in the Funny Bone; however, this one is large and yellow, and it will awaken Bowser from his knocked-out state early in the game.