The top reasons you would have more than one Amazon Affiliate Tracking Code on your affiliate site are:
You purchased an Amazon affiliate site from someone else and all the tracking codes were not changed out.
At some point, your tracking code changed and you did not change all the old Amazon store codes to the new one.
You may have wanted to use preferred tracking codes to track specific sales.
An example of this is maybe you wanted to track seasonal sales and created a tracking code for each season: