Hi Patrick,
Throughout my years of experience as a Biomedical Engineering Manager, we have had no such contamination problem. I am pretty sure your NICU department has a decontamination policy on hand in which the follow. It could be this policy is not followed accordingly as there is a frequency in replacing the incubator for the same baby every 7 days. Incubators go through a thorough decontamination once off the NICU Ward and filters must be cleaned and replaced often. In addition, the water reservoir must be decontaminated as well.
Good Luck