Subsites don't have the correct admin links and gives an error x 2

When a user logins into their site the Admin toolbar shows their subsite name with the comments bubble and the "+ New" menu which works great.

When the sub user clicks "New Post" the link shows/reads as http://mainsite.com/wp-admin/post-new.php, instead of http://mainsite.com/subsite/wp-admin/post-new.php. when clicked a WordPress message comes up (see attached)

Second error, which is possibly related. when I login as the Super admin and goto My sites. All the subsites are shown. The sites with the domain mapped show the mappeddomain.com/wp-admin, which is how it should work but the non mapped domains show mainsite.com/wp-admin on the dashboard links instead of mainsite.com/subsite/wp-admin?