I dont really see that as a "bug". That is the design of apt-get, and is a safety feature. Certain packages are held back to protect your system because it needs you to manually check that it's OK to do that.

Also.. you'd be surprised how many packages you don't see in the Application Manager that you'll see in apt-get.. and this is by design. A good portion of those packages your normal user has absolutely no need to deal with. Red Pill mode granted access to these.. as well as other things - and it obviously created enough of a stir as to get removed.

Anyway, doesn't surprise me at all that apt finds updates that Application Manager doesn't. It's just the way the system is setup.