Actually had this problem when I ordered the Kollector's Edition back in March through Amazon. Most sellers can't tell the difference, because they never actually pop the disc into an Xbox. Despite the fact that it says it's 2 discs on the case. I had to go through 3 different sellers before finding one that actually had both discs. So I understand how much of a pain it is to find out you got stuck with the bonus disc.
The bonus disc with the original Mortal Kombat arcade game is the disc that has the character that is on the cover of the Kollector's Edition you got(either Mileena, Scorpion, Baraka or Raiden). The actual MK Deception disc has the MK dragon logo on the game disc.
If you got it from a lowball, maybe contact who you got it from and ask if they have the actual game disc?