You must still have an infected machine somewhere on your network.
To isolate it, you can use the Risk Tracer feature in SEP.
To enable it:
Login to SEPM >> Policies >> Select your AV policy and edit it >> File System Auto-Protect tab >> Adavanced tab >> at the bottom, select the Risk Tracer button >> Enable it by ticking the box "Enable Risk Tracer"
To view logs:
Go to Monitors >> Logs >> set log type to Risk >> You can set your advanced settings as you wish >> click View Log >> up pops a list of infected machines and you can select any which are infected with Conficker and hit Details >> On the details page, look for the "Source Computer" and this should tell you the infected machine.
Remove it from the network, run the Conficker Removal tool, reboot and apply the patch.