This can happen for a lot of reasons. If you are on AX 2012 R3 CU9 and above, check the price of the item in price simulator to see if the price is coming properly.\\
Few things I would recommend to check :
Is this happening with all items or a speicific item ? - Check if a price group is attached to the store and same price group is used in the trade agreement.
Make sure that you activate Price/Discounts for groups in Sales and Marketing module - (Sales and marketing > Setup > Price/discount > Activate price/discount)
Verify, if you have a valid start date and Units in the trade agreement lines.
Confirrm if you the data has replicated to the store DB. (the data resides in ax.pricedisctable)