Bacteria thrive in warm moist environments with organic material present (an incubator exactly) and unless you are using aseptic technique throughout incubation your incubator is breeding something, but don’t panic, most bacteria are not bad, actually life on this planet might not be possible without them and other single cell organisms. This is also why chicks have immune systems. I doubt a naturally hatched chick is born into an environment anywhere near as clean as an average incubator yet birds don’t go extinct even so. Don’t panic! Clean up any obvious contamination or let it dry out, and if you are really worried, pull chicks every 4-6 hours at hatch to minimize contact with potential pathogens, add warm water a few minutes before opening the lid, be ready to just grab babies and be in and out quick which should minimize shrink wrap danger to hatching chicks.