Dont understand the status of Top secret

Around six months back I had a small security incident which was reported. I was new at the job, and was not aware of all the areas. My cell phone ended up going with me in my pocket to a classified area. The incident was reported, and it was closed and the FSO updated JPAS (minor issues since I was only in the area for few seconds). I recently applied for another position which requires Top secret clearance. I was told that my top secret clearance has a red flag. I am not sure what this is. They also said that my secret clearance is fine but they cannot proceed because the top secret has a red flag. If I recall the incident was resolved and JPAS was updated only with the incident. There was no action required on my end other than online facility training of appropriate areas.

What can I do to get rid of this red flag or better yet what this red flag is. Would the DOD automatically remove this red flag later. I can communicate to my FSO if needed. Can I do something to correct this red flag. What should I ask. Any tips or advise would be niceā€¦Thanks

Your situation sounds very confusing the way you have explained it. Why do you have more than one clearance at different levels? If you have a TS there would be no need for a Secret. The security incident would be treated the same for both levels. I would have your FSO dig into this.