I'm using Ubuntu 15.10 dev with apt 1.0.9.10ubuntu6 and if a specific package gets upgraded with "apt-get install" it gets also set to manual installed if it is an automatic installed package but this could be unexpected for the user. Maybe similar if the user tries to install an already up-to-date automatic installed package apt could tell the user then that the package got set to manual installed.
I'm using Ubuntu 15.10 dev with apt 1.0.9.10ubuntu6 and if a specific package gets upgraded with "apt-get install" it gets also set to manual installed if it is an automatic installed package but this could be unexpected for the user. Maybe similar if the user tries to install an already up-to-date automatic installed package apt could tell the user then that the package got set to manual installed.