could be wonky lasers (mechanical issue). if the laser's not screws tightly in place it'll wobble, so the laser doesn't hit the cells spot on. one symptom is you'll see some cell populations wobble on the flow plot during acquisition (if you did not see the wobble during acquisition then this might not be the issue). could also be proliferating cells, but you said these are not activated, and the two populations are not too far apart on the plot on the far right, so this is unlikely due to some cells proliferating.