Khan Academy has a few incredibly industrious users, also called Power Users, with typically more than 10,000,000 points. Some can no longer earn badges, or there is trouble with the notifications when they are earning them.
Currently, there is an upper limit to how many badges can be registered on an account. If you exceed this limit, you will see trouble with badge registrations. There is no known workaround, nor can you currently choose which badges will be dropped from your account to display more desirable ones.
We apologize for the issue. Khan Academy is looking into how to improve the experience for Power Users.