Domain Mapping bot crawl error (404) on subsites

Hello! I'm having an issue on the subsites of my multisite Wordpress install procentive.com where we are using the Domain Mapping plugin (the particular subsites having the issue are http://clinicaltrainingmanager.com/ , http://shop.procentive.com/ , http://customersuccess.procentive.com/ ).

The issue is that although the sites are working and displaying normally, when bots crawl those subsites they are seeing the sites returning a 404, so they are viewing the sites as invalid. We are in no way setting bots files to "nofollow" or anything like that, so it seems the issue is related to an error with how we are mapping those domains.

I have granted site access through the WPMUdev plugin portal. If you have any insight into what may be going on there, that would be much appreciated.

Thanks!
John Shields
Mere Agency