In many labs today, the primary staining process is completed manually through "dipping and dunking" slides into shared reagent baths.
The potential for cross contamination presents itself at multiple points in the process:
Sometimes, cross contamination is something a pathologist can "read through" or detect on his/her own because of obvious differences in tissue structure. Other times, the tissue fragments are too similar to tell the difference.
-Eric Platt, et al.
Tissue Floaters and Contaminants in the Histology Laboratory 3
Tissue contamination has been a long-time challenge in the anatomic pathology lab and, until recently, it was widely accepted as a part of the process. But it doesn't have to stay that way.
Automated, individualized staining greatly reduces the potential for cross contamination between slides and allows for better quality and consistency in comparison to what a lab can achieve with manual "dip and dunk" processes.
3: Platt, Eric, et al. "Tissue Floaters and Contaminants in the Histology Laboratory." Arch Pathol Lab Med. 2009 Vol. 133.