When upgrading ships I selected the button to do all the ones in the class and on more than one occasion my ballance went below 0 to a negative number but on some occasions, am i sure it went to below -50000 once, the next turn the ballance would then jump to -2000 then start counting as normal.

Is this:-

a ) a bug and so I am geting lots of upgrades for free?

or

b ) the way it works and your civ goes into some emergency econemy mode and resets to -2000 but the money comes from somewhere