Got this error when trying to upgrade from WebSphere Portal 6.0 to 7.0.
com.ibm.portal.puma.SchemaViolationException: EJPSG0053E: Puma requested entity type Group from VMM but received Entity.
This sets a record for one of the most unhelpful errors ever. It can be caused by a bad entry in LDAP - in my particular case, it was a few groups whose objectClasses (groupOfUniqueNames and top) had somehow been saved with base-64 encoding instead of as plain text, although the values themselves when decoded were correct. The same exact LDAP directory was also working fine with WebSphere 6.0.
One of IBM's pages implies that the configuration itself is broken - when in my case, the configuration was perfectly fine and the problem was a bad entry in LDAP. The error gives no help tracking down the broken entry.
Other IBM resources imply that the specific configuration issue is making sure that the group and user LDAP object classes are unique - i.e., don't use "top". In my case, I was doing pretty standard stuff - groupOfUniqueNames and inetOrgPerson.