This occurs when a Gateway is enrolled with 4.x portal systems that were previously integrated with a classic, 3.x Portal.
This can also be seen when a portal was migrated from 3.x to 4.x.
Some components from the previous portal are left behind on the Gateway that will need to be removed.
1) Log into the Gateway via ssh and locate the older assertions: ApiPortalIntegrationAssertion and ApiPortalDataLensAssertion
# cd /opt/SecureSpan/Gateway/runtime/modules/assertions
# ls -al | grep -i Portal
-r--r--r-- 1 layer7 layer7 1923558 May 30 2016 ApiPortalDataLensAssertion-8.4.00.aar
-r--r--r-- 1 layer7 layer7 682431 May 30 2016 ApiPortalIntegrationAssertion-8.4.00.aar
2) Move the assertions out of this folder to another location:
Be sure to only remove these two Portal assertions.
mv ApiPortalIntegrationAssertion-*.aar /home/ssgconfig
mv ApiPortalDataLensAssertion-* /home/ssgconfig
3) Restart the Gateway service
# service ssg restart
Duplicate APIs will remain on the Gateway and require manual cleanup. Newer published APIs will no longer duplicate.