This issue was first reported for One-dimensional physics, but affects a number of topics.
The tracker for One-dimensional physics on page https://www.khanacademy.org/science/physics is stuck on 37/38 after doing all the activities, while the tracker under Resume learning on the Leaner home page correctly shows 38/38.
We have been able to replicate the issue, which for this example seems to be connected to the Skill check at the top of the One-dimensional motion page.
As of now we have no workaround for changing the tracker on the topic page. We apologize for the issue.
Internal ticket: 221414272757015
Last updated Dec. 13th 2016