This sounds like a potential bug so probably best logged with BMC Support so they can investigate, but if you want community help, may I suggest you provide more information, such as:
1. Version of Control-M/Server and of Control-M/EM (in case this is a known bug fixed in a later version)
2. Does this problem re-occur or was it a once off issue?
3. Provide the full LOG of the Smart Folder (maybe it went to Ended OK and later to Executing, after a job in it was rerun or a job got ordered into it, but the GUI is not reflecting the status color correctly, which I would think is a bug).
4. Is the Smart Folder a Cyclic folder?
5. Are there any jobs in the Smart Folder that have the "End Folder" field checked? And if yes, have any of those completed?