I have a 2007 Xterra manual transmission and my vehicle does the same thing with people in the back seat.

It makes a thud / thunk noise over some dips or over some speed bumps.

The dealer says it's "the design" and they recreated the issue with both a new 2008 and my 2007. Seems like a poor design to me considering the Xterra is supposed to be rated to hold over 1000lbs including cargo.

This is a safety issue to me. The first time I heard the noise I thought I hit something in the road.