Something happened when Magneto forcibly removed all of the Adamantium from Logan’s skeleton. It unleashed something the Adamantium was holding back. His true nature.

Without the metal, his healing factor (which had been constantly working against the adamantium) went into overdrive and began to alter him. Overtime, he gradually became more animalistic and feral—losing his nose, teeth becoming sharper, his body and behavior becoming more bestial.

He was not Logan anymore. Only Wolverine. An animal.