My scenario was the opposite; Preview was running and was present in the Dock, but appeared not to be running as indicated by its absence from KM’s Applications Palette.
Yes - it is likely it was technically not running, but the system was pretending it was running, and thus the system knew to pretend its icon in the Dock, but the normal APIs don't show the running process.
I have the same issue, and Preview is definitely running — I've been using it to read a PDF.
☞ Update to the above: manually quitting and relaunching Preview did make it show up in the KM app switcher again. Maybe the system had terminated a dormant instance of Preview at some point, and then I relaunched/reactivated it by opening my PDF, but the relaunch for whatever reason didn't register with KM. In any case, before I manually quit and relaunched Preview I was actively using it (scrolling, etc.), but it wasn't visible in the switcher.
I think there are some cases where apps with strange activation modes (Preview and Calendar?) that can “sort of” quit when still apparently running cause Keyboard Maestro to get confused.