ClixSense will only show a referral in your downline that has activated their account. This means that someone you referred may have signed up under you but not be shown in your downline until they complete their profile.
If you have your account setup to send new referral notifications you will get a notice that your referral has signed up but until they activate their account they will not be shown under you. To check your account settings login and go to the Profile and Settings link.
Another issue could be that this person clicked another members referral link after clicking yours. This would set a new cookie and they would then become the referral of the last affiliate URL they clicked.