It only counts skylanders that are registered to the game file.
If you've used them on a different file or in the first game, then they would be linked to that file. You would then need to register it to the file you are using. This option is found under the stats menu for the Skylander.
Doing this will also deregister it for the other file, so it'd need to be reregistered back on the other file if you go back (primary reason for doing this would be to keep the elemental and exp bonuses for having so many skylanders).