Probably Lapu-lapu died of a very serious disease. Coz at that time there is no possible remedy or antidote to cure malignant diseases or abnormal physical conditions. Or maybe, he was attacked, killed at eaten by wild animals on his way to the forest, that is why there is no recorded time and event of his death. Even his whereabout is unknown to people he's been with during his time, after the death of Magellan.
It's not clear, but we know he was killed in the Battle of Mactan. By exactly who we don't know, because initial news reports that came out were sketchy. But the killing was generally attributed to Magellan even though there were no witnesses to verify that, simply because he was the leader of the visiting team.