If you explain that in your self assesment you certainly won't lose any marks as it demonstrates that you are completing the task very thouroughly indeed.

Yes indoors you would have to increase the ISO speed unless you have a fast (f1.4-f2.8 lens). Nothing wrong there but as I said a camera should give a correct exposure regardless of the ISO setting.

Personally I wouldn't be happy with a camera that routinely over exposes - any camera repair company could tell you if the camera's metering system is working correctly as will Nikon. You certainly shouldn't have to use exposure compensation to acheive a correct exposure to a grey card. My 50 year old Weston meter will acheive this so a new camera should! I'd get it checked out.