The main thing that tends to show far more mineral usage than it actually demands is missile production. I tend to make big queues of missiles so I dont have to worry about them, so Tritanium and Gallicite usage estimates by the program are often really huge.
The main thing you need to be concerned about underballing is fuel refining, because it only shows a year's worth of consumption. Watch your sorium levels carefully.
Neutronium is also a concern, since it tends to be consumed in huge bursts by retooling - sufficient stockpiles of neutronium are more guess than anything.