Hard to tell without having the art to examine, but my guess is that with a "right pupil" layer inside a "right pupil" group, both are auto-tagged Right Pupil. In that case the group will be the one that's controlled by Face (and the Rigging Issues panel should warn you that the layer one isn't matched to any behaviors). Since you have the layer crowned it will be on its own mesh. Still, that should move with its parent group, so I wouldn't expect it to be stuck. But try crowning the group instead of the layer, or making sure you have only one layer/group named "right pupil" (and same for left).
Sorry for my delayed reply. I'm not seeing any smoking gun there. If you're willing to DM me the .puppet file I should be able to figure it out.