From the Super Mario Wiki
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A nubbin is an inflammation-like protrusion that is found throughout Bowser's body. 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) will appear, which can cause a different effect from the regular nubbins (like powering up Bowser). 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.