I am having some trouble reproducing this; can you be a little more exact about the steps necessary to create this state from a new game?
With a brand new game, just waste a bunch of money (e.g. buying town properties). Once your net wealth falls from 250K to about 20K, the finance window shows 'Net wealth negative'.
Anyhow, this is a very trivial thing: I'd much rather you spent your effort on the waypoint and industry capacity issues, which do significantly affect gameplay.