My ex gets this too. I think it might just be from bacteria getting into the navel...like if water gets in it during showering and you don't dry it off. Moisture can irritate the skin to the point of bleeding. And since you're a guy, I don't think it's endometriosis.
My advice would be to make sure you dry off your belly button after getting it near water. Just wrap your finger in a towel and poke around in the navel...not so far that it hurts, but enough to dry it off. It should help.