First verify your return was accepted by the IRS. You can quickly find out if you did by checking your status. Make sure you wait at least 24 hours after acceptance before using Where's My Refund.
If it was accepted, make sure when checking your refund status on the Where's My Refund? site, to only enter your federal income amount, not federal and state combined.
If you are certain you are entering the correct information, social security number of primary taxpayer, filing status and amount of federal refund, check the IRS website in 24 hours as the sight updates once a day.