Bat guano carries Histoplasmosis is a disease you can get from exposure to bat guano (bat droppings).
you've failed not only GMPs, but preventative maintenance (doors, seals etc) and internal auditing (where you should have been able to see possible entry points)
Cover everything immediately. If possible re-route employees so they don't risk contaminating hairnets or make sure they leave on dirty PPE when travelling through and dispose of it once they are past
Remove the bat-then inspect, clean and sanitize and or dispose post inspection.
the fact the ceiling is really high actually makes it worse, contamination on the bat can now spread through the entire room on the air currents with relative ease