Some people believe that it is not waste, but dead zooxanthellae (which I guess could be considered waste, but it's not poop in the traditional sense). The zoox typically dies in transport because the nem isn't exposed to light. While we don't know for sure, I think people believe it's dead zoox because the nems aren't fed prior to transport, so there shouldn't be much, if any, solid waste. Furthermore, typical nem waste is stringy, not in pellet form as we see with newly acclimating nems.
My hypothesis is that this dead zoox begins to decay within the nem. It can sense the osmotic pressure within the transport bag which is why is doesn't purge while in the bag. Once it's in the QT or DT, it deflates in hopes of removing the dead zoox. As the same time, a bacterial infection begins to set in -- Cipro is used to combat this infection which allows the nem to purge the dead zoox.