In user multisite, the network main site Sitemap is pointing to a subsite sitemap: http://take.ms/TF5xP
The sitemap for that subsite 11 is showing all links of the network main site: http://take.ms/xryEW
Also, when user visits the network main site sitemap with his own network admin user (which is not "wpmudev"), the admin bar shows that the logged in user is "wpmudev": http://take.ms/R2bbT
Cleared site and server cache, didn't help. Even disabling the WP Super Cache didn't help.