One side of my headphones has started making
a vibrating/rattling noise that varies by the
frequency of the audio. I took it apart some
to see where it might be coming from
and it appears to be form inside the sealed
little speaker.
Has anyone else ever had this? Is it common?
Any idea what the problem is?
It's still under warranty. Has anyone had
experience with sending headphones
in for warranty work?

Send those cans in for warranty work!

What you're describing is probably a "blown" diaphram, meaning that the speaker element is either torn or partially detached from its moorings.