Resolution
By default, in a windows local connector aggregation, if Access Governance Suite finds any domain accounts that are part of the local group membership it returns them in the account aggregation as well. This leads to receiving the "System.NotImplementedException: Not implemented" error.
This feature can be disabled by adding the following value to the connector:
<entry key='disableNonLocalLookup' value="true"/>
Another workaround is to remove any domain level accounts from those local groups being aggregated.
The 5.2 code base is not vulnerable to this issue.