Did you use any liquid when cleaning the eggs? Honestly, I don't wash eggs before incubation. If you wash the eggs you are taking off the bloom, which is its natural protective coating. While the egg may look cleaner, there will still be bacteria/etc. on it that will then be able to access the embryo easier because there is no longer any protection. You can wipe it gently with a dry cloth to get the worst off, but I wouldn't apply any liquid at all.
There has been a lot of discussion on past posts about whether to wash or not to wash eggs, you may want to search it.
But yes, now that you know that it's present in your incubator due to the last batch, you will want to bleach it down before you use it again. It's good practice in general to do a bleach wash before and after each incubation.