When adding a SEPM Controller to the ATP's web interface, you add all of the required information for the SEPM and click OK. If the window stays up for too long and you then hit Cancel, the SEPM entry is added anyway.
There is an issue with the software that will implement the settings even if Cancel is clicked. The ATP does not check for duplicate entries of the same SEPM servers, so this can also lead to duplicate entries.
Delete duplicate entries in the SEPM connections list in ATP Manager, and also delete the entries in the Web Service Application Registration of SEPM. Reconnect when the corrections have been made to the connections in ATP Manager and wait for the window to close by itself.