It happens during Automate process - we have error reporting so we get alerted to these errors.
It happens on several sites, all have the same WP and PHP details which are as follows:
I know this is a really old thread but I had the exact same issue, and WPMU Dev support confirmed it was the same issue.
I believe Surbma simply did not comment out the "sunrise" line in wp-config, which you need to do after deactivating the plugin. Then they would have realised that it IS the domain mapping plugin causing the conflict.
In the end I just removed the plugin and used the WordPress 4.5 feature which allows you to map domains without a plugin: https://catapultthemes.com/mapping-a-domain-on-wordpress-4-5-multisite/