"Or they aren't staining it right, improper timing or over-rinsing. I don't know if the spores make it a little harder to stain with Gram stain. "If they can't run a Gram stain or have trouble staining & identifying a Bacillus, the lab needs to be shut down and the workers sent back for training. Seriously, Gram staining is micro 101. A hospital lab worker can just about do this in his or her sleep. Bacillus is one of the easiest bugs to stain and identify, at least at the Genus level.
Of course gram stain is micro 101 but there are many sources of potential error in that test. It's an easy test but one of the most error prone tests in clinical labs. Even the culture characteristics can affect the way the bacteria take up the stain.