[Suicide Junkie]

Things that don't show up in the budget are usually instant effects.
-retrofitting
-scrapping
-resource conVersion
-trade offers (not treaties, but item swaps)

Another possible way this could happen is if the host of a game has different files from yours. Your budget would think that you're making profit, but the host would calculate a different result.

I doubt it, but if you checked the budget, then added some one-turn build orders just before ending the turn, you might get this.

One more idea: finite resources. If you've got this set, and you've got some low values, your miners could be running out of resources to mine, thus not getting the full production the budget expects.