To understand Magellan's poor decision making, we need to set up the context of the events first. Before the Battle of Mactan, Magellan had just converted a major power in the island of Cebu, which was Rajah Humabon. When Rajah Humabon converted, he thus instructed all Datus (village chiefs below the Rajah) to convert as well, but one Datu did not comply, which was Lapu Lapu. Now, it seems that from Pigafetta's account, Humabon ordered Magellan to pacify Lapu Lapu, and Magellan accepted it, thinking that it would be a way to strengthen his image (and Spain's image) to the local powers.

Now, Pigafetta commented that Magellan had counted on his ships' cannons supporting him, but due to the rocks near Mactan's coast and the relative shallowness of water, his ships weren't able to get in range to support him. He couldn't even bring some of his musketeers that were guarding the boats that carried Magellan from his anchored ship way way beyond the shore.

Essentially, basing from Pigafetta's account, Magellan relied too much on the idea of the superiority of his firepower without considering that the terrain worked against his artillery platform, and that the very long distance between him and his support meant that he was essentially unable to make use of his one single advantage.