Please follow the instructions in the article I linked earlier (repeated below):
http://www.symantec.com/docs/TECH163349
The article provides steps and an executable tool, that will remove the HWID from the cloned machines.
Attached to the article is the "RepairClonedImage" tool. Run this on the machines that were cloned to rmove the HWID. After the tool is run, the next time the machines check into the SEPM they should generate a new SEP Client record and report separately. While these client records are individual and unique (because of teh new HWIDs) they will all be reporting the same machine name until you change them).
The article also provides instructions (Step 2) on how to run the RepairClonedImage tool on clients remotely using the CDW, which can be very useful.