User blog comment:Brianbreed/The Biggest Single Plot Hole in Mass Effect 2/@comment-82.35.187.133-20130623230526

And about the original NormNdy not having toilets - my guess it that, to stop and crew members from needing to leave their seats, they simply crapped into a bag and threw it into an the airlock during their break.

But then, why is there a bathroom in ME2? I suppose crew members not needing to leave their seats to make flight more safe was not necessary anymore. EDI could've taken care of their functions while they were doing their business.