they do a pretty good job with their automated system here at cgcookie, but every now and then you do get an issue like this in that the system is not recognizing that i watched this lesson in its entirety and crediting me accordingly.
it is undesirable not to receive credit for something you did, but this is precisely why they have included a manual way to mark lessons as complete; i recommend using this feature only as needed. if you hover over the eye icon next to the bookmark icon, then a popup will inform you that you can mark the lesson as complete; just click the icon and the system should update.