Microsoft has released the following KB article which includes a Hotfix:
FIX: Delta group discovery doesn’t remove resources from collections in System Center 2012 Configuration Manager SP2
Symptoms:
After you remove a previously discovered user or computer from a security group, delta group discovery does not remove that resource from a Configuration Manager collection as expected. This issue only affects delta discovery. A full discovery cycle removes resources from collections when they are removed from their corresponding security groups.
Full details: