This answer above by @amandala was the cause of my issue, though I couldn’t find the actual window anywhere to expand it. Even in Mission Control mode (three finger swipe up), no atom window was visible.
I ended up resolving it by navigating to
Zoom in the Atom application toolbar (i.e., menu bar at the top of the screen). I triggered Zoom for each of my windows and it brought each window back to normal size.