I learned about Kupffer cells the other day in biology class when our instructor was going over how the immune system works. These cells, along with T cells, destroy pathogens before they can cause disease in our bodies. So they're sort of like the army. They protect the body by working together with other components of the defense system.
As far as I understand though, sometimes, when the immune system is weak, the Kupffer cells aren't able to do their job as well. They are low in numbers or simply don't get the command to recognize and destroy pathogens. Other times, they do their job correctly, but other actors in the immune system don't and the pathogens are able to cause disease.
For example, after the Kupffer cells destroy pathogens, other cells have the job of getting rid of their remnants from the body. If that doesn't happen, these pathogens get into tissues and can cause the immune system to attack its own tissues! So Kupffer cells are just one piece of the puzzle. Everything has to work perfectly for the immune system do its job right and I find this really amazing.