I suspect this was the case, especially is the AA agent removed the KTN and added it back in (which usually fixes the issue). Personally, the last time I was selected for random screening was way back during the invitation-only TSA Pre-check pilot program with AA/DFW and DL/ATL which was a lonnnng time ago, so I do tend to forget that this is a thing.

Regarding the dreaded SSSS, as others have pointed out, it can be applied to any itinerary. I was quite surprised to see, in an AA non-rev Facebook group, that an employee even got an SSSS on a non-rev booking (lol!)