Lyric discussion by ebowtheletter 

There is no reference to Matthew Shephard. The album was recorded 3 months before the incident. Not just is the reference not clear but it is impossible based on facts.

@ebowtheletter

The album was released late oct. M. died mid oct. 1998. Also he died of brain stem dysfunction. Rostral part of brain stem = reptilian brain ("alligators"). M. died a sunday night from intracerebral bleeding. ("He bled 'til sunday night").

It's quite a coincidence, but Stipe himself denied that it was in reference to Matthew Shepard. And like ebow says, they recorded the take of the song that ended up on the album before the incident happened. They didn't go back in the middle of October to change the lyrics on a song, rerecord the song, repress all the copies they had prepared, and then ship it out a week later.

An error occured.